<PAGE>   1
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                   FORM 10-K/A

[X]    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES AND
       EXCHANGE ACT OF 1934

                    For the fiscal year ended DECEMBER 31, 1999

                                        or

[ ]    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
       EXCHANGE ACT OF 1934

                For the transition period from _______ to _______

                         Commission File Number: 1-13625

                        EOP OPERATING LIMITED PARTNERSHIP
             (Exact name of registrant as specified in its charter)


<TABLE>
<S>                                         <C>
                 DELAWARE                             36-4156801
      (State or other jurisdiction of              (I.R.S. Employer
      incorporation or organization)             Identification No.)
        TWO NORTH RIVERSIDE PLAZA,                      60606
       SUITE 2100, CHICAGO, ILLINOIS                  (Zip Code)
 (Address of principal executive offices)
</TABLE>

                                 (312) 466-3300
              (Registrant's telephone number, including area code)

           SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:

<TABLE>
<S>                                   <C>
                                         Name of each exchange on which
         Title of each class                       registered

                None                                  None

</TABLE>

            SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:

                       Units of Limited Partnership Interest

   Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (of for such shorter period that the
registrant was required to file such report), and (2) has been subject to such
filing requirements for the past 90 days.     [X]  Yes     [  ] No

   Indicate by check mark if disclosure of delinquent filers pursuant to
Item 405 of Regulation S-K is not contained herein, and will not be contained,
to the best of the registrant's knowledge, in definitive proxy or information
statements incorporated by reference in Part III of this Form 10-K or any
amendment to this Form 10-K. [ ]

   The aggregate market value of the Common Shares held by non-affiliates of the
registrant as of March 1, 2000 was $6,600,295,958.

                        DOCUMENTS INCORPORATED BY REFERENCE

   Portions of the registrant's proxy statement for the annual shareholders'
meeting to be held in 2000 are incorporated by reference into Part III.


<PAGE>   2

                                      PART IV

ITEM 14.  EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS OF FORM 8-K

  (a)(3)    Exhibits:

            Item 14(a)(3) is amended to renumber Exhibit 10.1 as 3.1.1 and add
            Exhibits 3.1.2 through 3.1.6 as set forth below:

<TABLE>
<CAPTION>
 Exhibit No.        Exhibit Description
 -----------        -------------------
<S>                 <C>
    2.1             Agreement and Plan of Merger, dated as of
                    February 11, 2000, among the Trust, the
                    Company, Cornerstone Properties Inc. and
                    Cornerstone Properties Limited Partnership
                    (incorporated herein by reference to Exhibit
                    2.1 to the Company's Current Report on Form
                    8-K dated February 11, 2000)

   3.1.1*           Agreement of Limited Partnership of the
                    Operating Partnership, dated as of July 3,
                    1997, as amended

   3.1.2**          Fifth Amendment to Agreement of Limited
                    Partnership of EOP Operating Limited
                    Partnership

   3.1.3**          Amendment to Agreement of Limited Partnership
                    of EOP Operating Limited Partnership

   3.1.4**          Seventh Amendment to Agreement of Limited
                    Partnership of EOP Operating Limited
                    Partnership

   3.1.5**          Eighth Amendment to Agreement of Limited
                    Partnership of EOP Operating Limited
                    Partnership

   3.1.6**          Tenth Amendment to Agreement of Limited
                    Partnership of EOP Operating Limited
                    Partnership

    4.1*            Indenture, dated as of September 2, 1997,
                    between the Operating Partnership and State
                    Street Bank and Trust Company

    4.2*            First Supplemental Indenture, dated as of
                    February 9, 1998, between the Operating
                    Partnership and State Street Bank and Trust
                    Company

    4.3             Form of 6.375% Note due 2003 (incorporated
                    herein by reference to Exhibit 4.4 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-47347))

    4.4             Form of 6.625% Note due 2005 (incorporated
                    herein by reference to Exhibit 4.5 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-47347))

    4.5             Form of 6.750% Note due 2008 (incorporated
                    herein by reference to Exhibit 4.6 of the
                    Company's Registration Statement of Form S-4
                    (Reg. No. 333-47347))

    4.6             Form of 7.250% Note due 2018 (incorporated
                    herein by reference to Exhibit 4.7 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-47347))

    4.7             Form of 6.376% Mandatory Par Put Remarketed
                    Securities due 2012 (incorporated herein by
                    reference to Exhibit 4.8 of the Company's
                    Registration Statement on Form S-4 (Reg. No.
                    333-47347))

    4.8             $30,000,000 7.24% Senior Note due 2004
                    (incorporated herein by reference to Exhibit
                    4.9 of the Company's Registration Statement on
                    Form S-4 (Reg. No. 333-47347))

    4.9             $50,000,000 7.36% Senior Note due 2005
                    (incorporated herein by reference to Exhibit
                    4.10 of the Company's Registration Statement
                    on Form S-4 (Reg. No. 333-47347))

    4.10            $50,000,000 7.44% Senior Note due 2006
                    (incorporated herein by reference to Exhibit
                    4.11 to the Company's Registration Statement
                    on Form S-4 (Reg. No. 333-47347))

    4.11            $50,000,000 7.41% Senior Note due 2007
                    (incorporated herein by
</TABLE>



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<TABLE>
<S>                 <C>
                    reference to Exhibit 4.12 to the Company's Registration
                    Statement on Form S-4 (Reg. No. 333-47347))

    4.12            Form of 6.50% Notes due 2004 (incorporated
                    herein by reference to Exhibit 4.3 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-61469))

    4.13            Form of 6.763% Notes due 2007 (incorporated
                    herein by reference to Exhibit 4.4 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-61469))

    4.14            Form of 7.25% Notes due 2028 (incorporated
                    herein by reference to Exhibit 4.5 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-61469))

    4.15            Form of 6.375% Notes due 2002 (incorporated
                    herein by reference to Exhibit 4.1 of the
                    Company's Current Report on Form 8-K filed
                    with the SEC on January 25, 1999)

    4.16            Form of 6.5% Notes due 2004 (incorporated
                    herein by reference to Exhibit 4.2 of the
                    Company's Current Report on Form 8-K filed
                    with the SEC on January 25, 1999)

    4.17            Form of 6.8% Notes due 2009 (incorporated
                    herein by reference to Exhibit 4.3 of the
                    Company's Current Report on Form 8-K filed
                    with the SEC on January 25, 1999)

    4.18            Form of 7.5% Notes due April 19, 2029
                    (incorporated herein by reference to Exhibit
                    4.23 of the Company's Current Report on Form
                    8-K filed with the SEC on April 19, 1999)

    4.19            Form of $400,000,000 8.375% Note due March 15,
                    2006 (incorporated herein by reference to
                    Exhibit 4.25 of the Company's Form 8-K dated
                    March 24, 2000)

    4.20            Form of $100,000,000 8.375% Note due March 15,
                    2006 (incorporated herein by reference to
                    Exhibit 4.26 of the Company's Form 8-K dated
                    March 24, 2000)

    4.21+           Second Amended and Restated Revolving Credit
                    Facility $1 Billion Revolving Credit Facility
                    dated as of May 29, 1998 (incorporated by
                    reference to Exhibit 4.22 to the Company's
                    Form 10-K for the year ended December 31, 1998)

    4.22+           First Amendment to Second Amended and Restated
                    Revolving Credit Agreement

    4.23+           Fixed Rate Promissory Note with The Chase
                    Manhattan Bank
</TABLE>


                                       3

<PAGE>   4

<TABLE>
<S>                 <C>
    12.1+           Statement Regarding Computation of Ratios

    21.1+           List of Subsidiaries

    23.1+           Consent of Independent Auditors

                    Power of Attorney (included in signature page
    24.1+           on Form 10-K)

    27.1+           Financial Data Schedule


*    Incorporated herein by reference to the same-numbered exhibit
     to the Trust's Annual Report on Form 10-K for the year ended
     December 31, 1997, as amended

**   Incorporated herein by reference to Exhibits 10.1.2 through 10.1.6,
     respectively, to the Trust's Annual Report on Form 10-K for the year ended
     December 31, 1999, as amended

+    Previously filed.
</TABLE>


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<PAGE>   5


                                    SIGNATURES

      Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, as amended, the Registrant has duly caused this report to
be signed on its behalf by the undersigned, thereunto duly authorized, in
Chicago, Illinois, as of the 11th day of May, 2000.

                                 EOP OPERATING LIMITED PARTNERSHIP

                                 By:     Equity Office Properties Trust, as
                                         general partner

                                 By:     /s/ STANLEY M. STEVENS
                                         --------------------------
                                         Stanley M. Stevens
                                         Executive Vice President,
                                         Chief Legal Counsel and
                                         Secretary




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<PAGE>   6



                                      EXHIBIT INDEX

<TABLE>
<CAPTION>
 Exhibit No.        Exhibit Description
 -----------        -------------------
<S>                 <C>
    2.1             Agreement and Plan of Merger, dated as of
                    February 11, 2000, among the Trust, the Company,
                    Cornerstone Properties Inc. and Cornerstone
                    Properties Limited Partnership (incorporated
                    herein by reference to Exhibit 2.1 to the
                    Company's Current Report on Form 8-K dated
                    February 11, 2000)

   3.1.1*           Agreement of Limited Partnership of the
                    Operating Partnership, dated as of July 3, 1997,
                    as amended

   3.1.2**          Fifth Amendment to Agreement of Limited
                    Partnership of EOP Operating Limited Partnership

   3.1.3**          Amendment to Agreement of Limited Partnership of
                    EOP Operating Limited Partnership

   3.1.4**          Seventh Amendment to Agreement of Limited
                    Partnership of EOP Operating Limited Partnership

   3.1.5**          Eighth Amendment to Agreement of Limited
                    Partnership of EOP Operating Limited Partnership

   3.1.6**          Tenth Amendment to Agreement of Limited
                    Partnership of EOP Operating Limited Partnership

    4.1*            Indenture, dated as of September 2, 1997,
                    between the Operating Partnership and State
                    Street Bank and Trust Company

    4.2*            First Supplemental Indenture, dated as of
                    February 9, 1998, between the Operating
                    Partnership and State Street Bank and Trust
                    Company

    4.3             Form of 6.375% Note due 2003 (incorporated
                    herein by reference to Exhibit 4.4 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-47347))

    4.4             Form of 6.625% Note due 2005 (incorporated
                    herein by reference to Exhibit 4.5 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-47347))

    4.5             Form of 6.750% Note due 2008 (incorporated
                    herein by reference to Exhibit 4.6 of the
                    Company's Registration Statement of Form S-4
                    (Reg. No. 333-47347))

    4.6             Form of 7.250% Note due 2018 (incorporated
                    herein by reference to Exhibit 4.7 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-47347))

    4.7             Form of 6.376% Mandatory Par Put Remarketed
                    Securities due 2012 (incorporated herein by
                    reference to Exhibit 4.8 of the Company's
                    Registration Statement on Form S-4 (Reg. No.
                    333-47347))

    4.8             $30,000,000 7.24% Senior Note due 2004
                    (incorporated herein by reference to Exhibit 4.9
                    of the Company's Registration Statement on Form
                    S-4 (Reg. No. 333-47347))

    4.9             $50,000,000 7.36% Senior Note due 2005
                    (incorporated herein by reference to Exhibit
                    4.10 of the Company's Registration Statement on
                    Form S-4 (Reg. No. 333-47347))

    4.10            $50,000,000 7.44% Senior Note due 2006
                    (incorporated herein by reference to Exhibit
                    4.11 to the Company's Registration Statement on
                    Form S-4 (Reg. No. 333-47347))

    4.11            $50,000,000 7.41% Senior Note due 2007
                    (incorporated herein by reference to Exhibit
                    4.12 to the Company's Registration Statement on
                    Form S-4 (Reg. No. 333-47347))

    4.12            Form of 6.50% Notes due 2004 (incorporated
                    herein by reference to Exhibit 4.3 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-61469))
</TABLE>

                                        6

<PAGE>   7

<TABLE>
<S>                 <C>
    4.13            Form of 6.763% Notes due 2007 (incorporated
                    herein by reference to Exhibit 4.4 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-61469))

    4.14            Form of 7.25% Notes due 2028 (incorporated
                    herein by reference to Exhibit 4.5 of the
                    Company's Registration Statement on Form S-4
                    (Reg. No. 333-61469))

    4.15            Form of 6.375% Notes due 2002 (incorporated
                    herein by reference to Exhibit 4.1 of the
                    Company's Current Report on Form 8-K filed with
                    the SEC on January 25, 1999)

    4.16            Form of 6.5% Notes due 2004 (incorporated herein
                    by reference to Exhibit 4.2 of the Company's
                    Current Report on Form 8-K filed with the SEC on
                    January 25, 1999)

    4.17            Form of 6.8% Notes due 2009 (incorporated herein
                    by reference to Exhibit 4.3 of the Company's
                    Current Report on Form 8-K filed with the SEC on
                    January 25, 1999)

    4.18            Form of 7.5% Notes due April 19, 2029
                    (incorporated herein by reference to Exhibit
                    4.23 of the Company's Current Report on Form 8-K
                    filed with the SEC on April 19, 1999)

    4.19            Form of $400,000,000 8.375% Note due March 15,
                    2006 (incorporated herein by reference to
                    Exhibit 4.25 of the Company's Form 8-K dated
                    March 24, 2000)

    4.20            Form of $100,000,000 8.375% Note due March 15,
                    2006 (incorporated herein by reference to
                    Exhibit 4.26 of the Company's Form 8-K dated
                    March 24, 2000)

    4.21+           Second Amended and Restated Revolving Credit
                    Facility $1 Billion Revolving Credit Facility
                    dated as of May 29, 1998 (incorporated by
                    reference to Exhibit 4.22 to the Company's Form
                    10-K for the year ended December 31, 1998)


    4.22+           First Amendment to Second Amended and Restated
                    Revolving Credit Agreement

    4.23+           Fixed Rate Promissory Note with The Chase
                    Manhattan Bank
</TABLE>


                                       7

<PAGE>   8

<TABLE>
<S>                 <C>
    12.1+           Statement Regarding Computation of Ratios

    21.1+           List of Subsidiaries

    23.1+           Consent of Independent Auditors

    24.1+           Power of Attorney (included in signature page on
                    Form 10-K)

    27.1+           Financial Data Schedule


*      Incorporated herein by reference to the same-numbered exhibit
       to the Company's Annual Report on Form 10-K for the year
       ended December 31, 1997, as amended

**     Incorporated herein by reference to Exhibits 10.1.2 through
       10.1.6, respectively, to the Trust's Annual Report on Form 10-K
       for the year ended December 31, 1999, as amended

+      Previously filed.
</TABLE>


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