UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Amendment No. 2

to

SCHEDULE 13D

Under the Securities Exchange Act of 1934

ENBRIDGE ENERGY PARTNERS, L.P.

(Name of Issuer)

Class A Common Units

(Title of Class of Securities)

29250R 10 6

(CUSIP Number)

E. Chris Kaitson

Vice President—Law and Assistant Secretary

1100 Louisiana, Suite 3300

Houston, Texas 77002

(713) 821-2000

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

May 8, 2013

(Date of Event which Requires Filing of This Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), Rule 13d-1(f) or Rule 13d-1(g), check the following box:  ¨

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7(b) for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934, as amended, (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

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Schedule 13D/A

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Schedule 13D/A

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Schedule 13D/A

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This Amendment No. 2 to Schedule 13D corrects the I.R.S. Identification No. of Enbridge Energy Company, Inc. and amends Items 2, 3, 4, 5, 6 and 7 of the Schedule 13D filed by Enbridge Inc., IPL System Inc., Enbridge Pipelines Inc. and Enbridge Energy Company, Inc. with the Securities and Exchange Commission on December 11, 2008 (the “Original Schedule 13D”), as amended by Amendment No. 1 to the Original Schedule 13D filed by Enbridge Inc., IPL System Inc., Enbridge Pipelines Inc. and Enbridge Energy Company, Inc. with the Securities and Exchange Commission on October 21, 2009.

Item 2. Identity and Background

The information previously provided in response to this Item 2 is hereby amended by replacing the text thereof in its entirety with the following:

This Schedule 13D, as amended, is filed jointly pursuant to Rule 13d-1(k)(1) by Enbridge Inc., a Canadian corporation (“Enbridge”), IPL System Inc., an Alberta corporation (“IPL”), Enbridge Pipelines Inc., a Canadian corporation (“EPI”), and Enbridge Energy Company, Inc., a Delaware corporation (“EECI” and, together with Enbridge, IPL and EPI, the “Reporting Persons”), pursuant to a joint filing statement, which is attached to this Schedule 13D, as amended, as Exhibit A.

The address of the principal offices of each of Enbridge, IPL and EPI is 3000, 425–First Street S.W., Calgary, Alberta, Canada T2P 3L8. The address of the principal office of EECI is 1100 Louisiana, Suite 3300, Houston, Texas 77002.

Enbridge is an energy transportation, distribution and related services provider. Enbridge’s principal business segments are: (1) the Liquids Pipelines segment and (2) the Gas Distributions and Services segment. The Liquids Pipelines segment includes the operation of Enbridge’s mainline crude oil and liquids pipeline system, and feeder pipelines in Canada and the United States. Enbridge’s wholly-owned subsidiary EPI owns and operates the Canadian portion of the Enbridge crude oil mainline and operates the U.S. portion of the mainline—the Lakehead System. Enbridge has an indirect 30.2% interest in the Issuer, which owns the Lakehead System. Enbridge’s Gas Distribution and Services segment consists primarily of gas utility operations that serve residential, commercial, industrial and transportation customers in central and eastern Ontario. The core of the Gas Distribution & Services segment is Enbridge Gas Distribution, which is Canada’s largest natural gas distribution utility. IPL is a holding company and a wholly-owned subsidiary of Enbridge. EPI is a liquid hydrocarbon pipeline transportation provider and a wholly-owned subsidiary of IPL. EECI is an indirectly-owned subsidiary of IPL and holds the general partner interest in the Issuer.

Information relating to the directors and executive officers of the Reporting Persons is contained in Schedule 1 attached hereto and is incorporated herein by reference.

During the last five years, none of the Reporting Persons or, to the undersigned’s knowledge, any of the persons listed on Schedule 1 hereto has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors). During the last five years, none of the Reporting Persons or, to the undersigned’s knowledge, any of the persons listed on Schedule 1 hereto has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

Item 3. Source and Amount of Funds or Other Consideration

The information previously provided in response to this Item 3 is hereby amended by adding the following:

On May 8, 2013, the Issuer issued and sold 48,000,000 Series 1 Preferred Units to EECI at a purchase price of $25.00 per Series 1 Preferred Unit. These Series 1 Preferred Units were issued and sold by the Issuer in a private transaction exempt from registration under Section 4(2) of the Securities Act of 1933, as amended (the “Securities Act”). EECI paid $1.2 billion to purchase the Series 1 Preferred Units, which purchase price was funded by Enbridge in part from its working capital ($700 million) and in part through a drawdown on one of Enbridge’s credit facilities ($500 million). The credit facility is a U.S. Dollar-denominated revolving credit facility dated January 10, 2012 (as further amended) and maturing on January 10, 2015 and entered into by Enbridge, as the borrower, and a syndicate of lenders, with Toronto-Dominion Bank as Administrative Agent. Net proceeds of the private placement to the Issuer were approximately $1.2 billion, as no expenses were deducted from the proceeds.

The Series 1 Preferred Units are convertible by the holder of such units and redeemable at the Issuer’s option, in each case under certain circumstances. On or after June 1, 2016, at the sole option of the holder of the Series 1 Preferred Units, the Series 1 Preferred Units may be converted into Class A Common Units, in whole or in part, at a conversion price of $25.00 per unit plus any accrued, accumulated and unpaid distributions (excluding certain distributions that were deferred for the first full eight quarters ending June 30, 2015 (the “Payment Deferral”)) divided by $27.78 (as adjusted for splits, combinations and unit distributions). The Series 1 Preferred Units are redeemable, in whole or in part, at the Issuer’s option on the five year anniversary of the issuance and every fifth year thereafter, at a redemption price of $25.00 per unit plus any accrued, accumulated and unpaid distributions (including the Payment Deferral). At all other times, redemption of the Series 1 Preferred Units, in whole or in part, is permitted only if (i) the Issuer uses the net

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proceeds from incurring debt and issuing equity (including assets sales) in equal amounts to redeem such Series 1 Preferred Units, (ii) a material change in the current tax treatment of the Series 1 Preferred Units occurs or (iii) the rating agencies’ treatment of the equity credit for the Series 1 Preferred Units is reduced by 50% or more.

Item 4. Purpose of Transaction

The information previously provided in response to this Item 4 is hereby amended by replacing the text thereof in its entirety with the following:

EECI acquired the right to acquire the Class A Common Units underlying the Series 1 Preferred Units upon conversion of the Series 1 Preferred Units as reported pursuant hereto for investment purposes. EECI and/or the Reporting Persons may acquire additional Class A Common Units (including those underlying Series 1 Preferred Units), or dispose of some or all of such Class A Common Units, from time to time, depending upon price, market conditions and other factors.

None of the Reporting Persons has any plan or proposal that relates to or that would result in:

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Item 5. Interest in Securities of the Issuer

The information previously provided in response to this Item 5 is hereby amended by replacing the text thereof in its entirety with the following:

Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer

The information previously provided in response to this Item 6 is hereby amended by replacing the text thereof in its entirety with the following:

The 16,250,000 Class A Common Units purchased by EECI on December 4, 2008 were purchased by EECI pursuant to the Class A Common Unit Purchase Agreement, dated November 17, 2008, by and between the Issuer and EECI. The 21,245 Class A Common Units purchased by EECI on October 14, 2009 were purchased by EECI pursuant to the Class A Common Unit Purchase Agreement, dated October 14, 2009, by and between the Issuer and EECI. In addition, on October 14, 2009, 6,987,923.633319 of the Issuer’s Class C Units that were held by EECI converted into 6,987,923 Class A Common Units. The Fifth Amended and Restated Agreement of Limited Partnership of the Issuer, dated as of May 8, 2013 (as used herein, the “partnership agreement”), contains various provisions with respect to the Class A Common Units governing, among other matters, distributions, transfers and allocations of profits and losses to partners.

On May 7, 2013, the Issuer and EECI entered into a Series 1 Preferred Unit Purchase Agreement (the “Unit Purchase Agreement”). Under the terms of the Unit Purchase Agreement, the Issuer issued and sold to EECI 48,000,000 Series 1 Preferred Units. The purchase price for the Series 1 Preferred Units was $25.00 per unit.

The Series 1 Preferred Units are entitled to annual cash distributions of 7.50% of the issue price, which is subject to reset every five years. These distributions are senior to distributions of cash to other partnership units. In addition, quarterly cash distributions will not be payable on the Series 1 Preferred Units during the first full eight quarters ending June 30, 2015, and instead will accrue and accumulate (the “Payment Deferral”) and be payable upon the earlier of the fifth anniversary of the issuance of such Series 1 Preferred Units or the redemption of such Series 1 Preferred Units.

On or after June 1, 2016, at the sole option of the holder of the Series 1 Preferred Units, the Series 1 Preferred Units may be converted into Class A Common Units, in whole or in part, at a conversion price of $25.00 per unit plus any accrued, accumulated and unpaid distributions (excluding the Payment Deferral) divided by $27.78 (as adjusted for splits, combinations and unit distributions). The Series 1 Preferred Units are redeemable, in whole or in part, at the Issuer’s option on the five year anniversary of the issuance and every fifth year thereafter, at a redemption price of $25.00 per unit plus any accrued, accumulated and unpaid distributions (including the

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Payment Deferral). At all other times, redemption of the Series 1 Preferred Units, in whole or in part, is permitted only if (i) the Issuer uses the net proceeds from incurring debt and issuing equity (which includes asset sales) in equal amounts to redeem such Series 1 Preferred Units, (ii) a material change in the current tax treatment of the Series 1 Preferred Units occurs or (iii) the rating agencies’ treatment of the equity credit for the Series 1 Preferred Units is reduced by 50% or more, all at a redemption price of $25.00 per unit plus any accrued, accumulated and unpaid distributions (including the Payment Deferral).

In the event of a merger or other extraordinary transaction involving the Issuer, the Series 1 Preferred Units are, at the option of the holder of such units, convertible into Class A Common Units or such holders will be entitled to receive the consideration they would have received in such transaction as if their Series 1 Preferred Units had converted into Class A Common Units immediately prior to such transaction. The holders of Series 1 Preferred Units will vote together with the Class A Common Units on an as-converted basis. The Series 1 Preferred Units will be entitled to vote as a separate class on any matter that adversely affects the rights, privileges or preferences of the Series 1 Preferred Units in any material respect or as required by law. The Issuer also cannot issue any additional Series 1 Preferred Units or securities that are senior or pari passu with the Series 1 Preferred Units, in respect of distributions and liquidations, unless EECI, the general partner of the Issuer, and the holders of a majority of the outstanding Series 1 Preferred Units approve such issuance. The Series 1 Preferred Units will be transferable subject to compliance with securities laws and certain other restrictions set forth in the partnership agreement. The partnership agreement contains various other provisions with respect to the Series 1 Preferred Units governing, among other matters, allocations of profits and losses to partners.

The Unit Purchase Agreement contains customary representations and warranties of the Issuer and EECI and customary covenants for a transaction of this kind.

Under the Unit Purchase Agreement and subject to certain limitations and survival periods, the Issuer has agreed to indemnify EECI and its affiliates, officers, directors, members, managers, employees and agents for certain breaches of the Issuer’s representations, warranties and covenants, and EECI has agreed to indemnify the Issuer and its affiliates, officers, directors, members, managers, employees and agents for certain breaches of EECI’s representations, warranties and covenants.

The closing of the transactions contemplated by the Unit Purchase Agreement was subject to typical conditions, including, among other conditions, (i) the absence of any law or order prohibiting the consummation of the transactions under the Unit Purchase Agreement and (ii) the execution of the partnership agreement and a registration rights agreement. The transactions contemplated by the Unit Purchase Agreement closed on May 8, 2013, which is the date that the Series 1 Preferred Units were issued to EECI.

In addition to the 89,719,646 Class A Common Units of the Issuer owned by EECI, EECI owns 7,825,500 Class B Common Units of the Issuer and a 2.0 percent general partner interest in the Issuer.

For a description of the contracts, arrangements, understandings or relationships among the Reporting Persons and between such persons and the Issuer and others, please read “Certain Relationships and Related Transactions, and Director Independence” in the Annual Report on Form 10-K for the year ended December 31, 2012 of the Issuer and the information reported in Items 1.01 and 5.03 of the Issuer’s Current Report on Form 8-K filed on May 13, 2013, each of which is incorporated herein by reference.

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Item 7. Material to Be Filed as Exhibits

The information previously provided in response to this Item 6 is hereby amended by replacing the text thereof in its entirety with the following:

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SIGNATURES

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Dated: May 16, 2013

Schedule 1

INFORMATION CONCERNING THE DIRECTORS AND

EXECUTIVE OFFICERS OF ENBRIDGE INC.

Set forth below are the name, citizenship and the present principal occupation and/or employment of each director and executive officer of Enbridge Inc. The principal business address for each individual listed below, is 3000, 425–First Street S.W., Calgary, Alberta, Canada T2P 3L8.

INFORMATION CONCERNING THE DIRECTORS

AND EXECUTIVE OFFICERS OF IPL SYSTEM INC.

Set forth below are the name, citizenship and the present principal occupation and/or employment of each director and executive officer of IPL System Inc. The principal business address for each individual listed below, is 3000, 425–First Street S.W., Calgary, Alberta, Canada T2P 3L8.

INFORMATION CONCERNING THE DIRECTORS

AND EXECUTIVE OFFICERS OF ENBRIDGE PIPELINES INC.

Set forth below are the name, citizenship and the present principal occupation and/or employment of each director and executive officer of Enbridge Pipelines Inc. The principal business address for each individual listed below, is 3000, 425–First Street S.W., Calgary, Alberta, Canada T2P 3L8.

INFORMATION CONCERNING THE DIRECTORS

AND EXECUTIVE OFFICERS OF ENBRIDGE ENERGY COMPANY, INC.

Set forth below are the name, citizenship and the present principal occupation and/or employment of each director and executive officer of Enbridge Energy Company, Inc. The principal business address for each individual listed below, is 1100 Louisiana, Suite 3300, Houston, Texas 77002.