<PAGE>

                                                                     Exhibit 3.2

                            Certificate of Amendment
                                       of
                          Certificate Of Incorporation
                                       of
                                Clark USA, Inc.


                   -----------------------------------------

                   Adopted in accordance with the provisions
                   of Section 242 of the General Corporation
                          Law of the State of Delaware

                   -----------------------------------------


     We, Paul D. Melnuk, President and Chief Executive Officer, and Patrick
F. Heider, Secretary, of CLARK USA, INC., a corporation organized and existing
under the laws of the State of Delaware (the "Corporation"), hereby certify as
follows:

     FIRST:  That the Certificate of Incorporation of the Corporation was
filed by the Secretary of State of the State of Delaware on the 24th day of
October, 1988.

     SECOND:  That Article 4 of the Certificate of Incorporation of
the Corporation has been amended as follows:

          ARTICLE 4.  The total number of shares of capital stock which the
     Corporation shall have the authority to issue is 56,164,597 shares
     consisting of (a) 51,164,597 shares of common stock, par value $.01, per
     share of which (i) 39,875,000 shares shall be designated "Common Stock,"
     (ii) 10,162,509 shares shall be designated as "Class A. Common Stock,"
     (iii) 562,500 shares shall be designated "Class B Common Stock," and (iv)
     564,588 shares shall be designated "Class C Common Stock"; and (b)
     5,000,000 shares of "Preferred Stock," par value $.01 per share.
<PAGE>

          A.  Preferred Stock

               1.  Issuance.  The Board of Directors is authorized, subject to
     limitations prescribed by law, to provide for the issuance of shares of
     Preferred Stock in one or more Class, to establish the number of shares to
     be included in each such Class, and to fix the designations, powers,
     preferences, and rights of the shares of each such Class, and any
     qualifications, limitations, or restrictions thereof.

          B.  Common Stock

               1.  Dividends.  Subject to the preferential rights, if any, of
     the Preferred Stock, the holders of shares of Common Stock shall be
     entitled to receive, when and if declared by the Board of Directors, out of
     the assets of the Corporation which are by law available therefor,
     dividends payable either in cash, in property or in shares of capital
     stock.

               2.  Voting Rights.  At every annual or special meeting of
     stockholders of the Corporation, every holder of Common Stock shall be
     entitled to one vote, voting together with the holders of the Class A
     Common Stock, Class B Common Stock and Class C Common Stock, in person or
     by proxy, for each share of Common Stock standing in his or her name on the
     books of the Corporation; provided that the holders of Common Stock shall
     have no voting rights with respect to matters reserved (by law or by
     agreement with the Corporation) solely for any other class of capital
     stock.

               3.  Liquidation, Dissolution, or Winding Up.  In the event of any
     voluntary or involuntary liquidation, dissolution, or winding up of the
     affairs of the Corporation, after payment or provision for payment of the
     debts and other liabilities of the Corporation and of the preferential
     amounts, if any, to which the holders of Preferred Stock, Class A Common
     Stock or Class C Common Stock shall be entitled, the holders of all
     outstanding shares of Common Stock shall be entitled to share ratably with
     Class A Common Stock and the Class C Common Stock in the remaining assets
     of the Corporation.

                                       2
<PAGE>

          C.  The Class A Common Stock

               1.  Dividends.  Subject to the preferential rights, if any, of
     the Preferred Stock, the holders of Class A Common Stock shall be entitled
     to receive the same dividends or distributions per share, whether payable
     in cash, in property, or in shares of capital stock, as may be declared and
     paid on the Common Stock, and the Board of Directors may not declare or pay
     any other dividend or distribution with respect to the Class A Common
     Stock.  Any dividend or distribution paid on the Class A Common Stock shall
     be paid pro-rata with the Common Stock and shall be paid in immediately
     available funds in such manner as the holders of Class A Common Stock shall
     reasonably request.

               2.  Voting Rights.  At every annual or special meeting of
     stockholders of the Corporation, every share of Class A Common Stock shall
     entitle the holder thereof to one vote, voting together with the holders of
     the Common Stock, Class B Common Stock and Class C Common Stock, on all
     matters submitted to a vote of the holders of Common Stock, Class B Common
     Stock or Class C Common Stock, in person or by proxy, in the same manner
     and with the same effect as the holders of Common Stock, Class B Common
     Stock and Class C Common Stock; provided that the holders of Class A Common
     Stock shall have no voting rights with respect to matters reserved (by law
     or by agreement with the Corporation) solely for any other class of capital
     stock.

               3.  Conversion.  The holder of any shares of Class A Common Stock
     shall have the right, at any time or from time to time, to convert any or
     all of such holder's shares of Class A Common Stock into an equal number of
     shares of Common Stock.

               4.  Anti-Dilution.  The Corporation shall not take any action
     (including, without limitation, payment of a dividend or distribution on
     the capital stock, subdividing or reclassifying any outstanding shares of
     capital stock, issuing capital stock at less than its book value, a merger
     or consolidation, or any other action) which may have the effect of
     diluting the value of the Class A Common Stock (or the capital stock into
     which the Class A Common Stock is convertible), except with the prior
     written consent of Tiger Management Corporation ("TMC") (which consent
     shall not be unreasonably withheld so long as TMC is satisfied that
     appropriate anti-dilution protection and adjustments have been put into
     effect by the Company with respect to such capital stock).

                                       3
<PAGE>

               5.  Liquidation, Dissolution or Winding Up.  (a)  In the event of
     any voluntary or involuntary liquidation, dissolution, or winding-up of the
     affairs of the Corporation (a "Liquidation") on or prior to the Public
     Float Target Date (as defined in (c) below), the holders of shares of Class
     A Common Stock shall be entitled to share ratably, with the holders of
     Common Stock and (to the extent and on the basis set forth below in
     connection with the Class C Common Stock) the Class C Common Stock, in the
     remaining assets of the Corporation available for distribution after
     payment or provision for payment of the debts and other liabilities of the
     Corporation and of the preferential amounts, if any, to which the holders
     of Preferred Stock shall be entitled (the "Liquidation Proceeds"); provided
     that if the Liquidation Proceeds are less than the product of (i) the total
     number of shares of Common Stock and Class A Common Stock (including the
     number of shares of Class A Common Stock into which the Class C Common
     Stock are deemed to be converted as set forth below in connection with the
     Class C Common Stock) entitled to share in the Liquidation Proceeds
     multiplied by (ii) the Purchase Price (as defined in (c) below), then (a)
     first, the holders of the Class A Common Stock and (to the extent and on
     the basis set forth below in connection with the Class C Common Stock) and
     the Class C Common Stock shall have first priority with respect to the
     Liquidation Proceeds in an amount per share of Class A Common Stock held
     (or deemed to be held as set forth below in connection with the Class C
     Common Stock) by each holder of Class A Common Stock and Class C Common
     Stock equal to the applicable Purchase Price and (b) then, the holders of
     the Common Stock shall share ratably in any remaining Liquidation Proceeds.

               (b) In the event of any Liquidation after the Public Float Target
     Date, the holders of shares of Class A Common Stock shall be entitled to
     share ratably, with the holders of Common Stock and (to the extent and on
     the basis set forth below in connection with the Class C Common Stock) the
     Class C Common Stock, in the Liquidation Proceeds.

               (c) "Public Float Target Date" shall mean the first date
     following the initial public offering of Common Stock on which the
     aggregate market value of the Common Stock held by persons other than Tiger
     Management Corporation ("TMC"), affiliates of TMC, The Horsham Corporation
     ("Horsham"), affiliates of Horsham and employees of the Corporation exceeds
     $150 million.

                                       4
<PAGE>

          The "Purchase Price" means, (a) if the Liquidation occurs prior to the
     Conversion Date (as hereinafter defined), $13.33 per share and (b) if the
     Liquidation occurs after the Conversion Date, the Share Price for the
     applicable Conversion Level (as defined below) as set forth in the chart in
     Article 4.D.3(e) below.


          D.  Class B Common Stock and the Class C Common Stock

               1.  Dividends.  Subject to the preferential rights, if any, of
     the Preferred Stock, the holders of Class B Common Stock and Class C Common
     Stock shall be entitled to receive the same dividends or distributions per
     share, whether payable in cash, in property or in shares of capital stock
     as may be, declared and paid on the Common Stock or the Class A Common
     Stock, and the Board of Directors may not declare or pay any other dividend
     or distribution with respect to the Class B Common Stock or the Class C
     Common Stock. Any dividend on the Class B Common Stock or the Class C
     Common Stock shall be paid pro-rata with the Common Stock and the Class A
     Common Stock and shall be paid in immediately available funds in such
     manner as the holders of Class B Common Stock and Class C Common Stock
     shall reasonably request.

               2.  Voting Rights.  In addition to the rights specified elsewhere
     in this Section and any other rights provided in the Corporation's by-laws
     or by law, at every annual or special meeting of stockholders of the
     Corporation, every holder of Class B Common Stock and Class C Common Stock
     shall entitle the holder thereof to 1/10th of one vote, voting together
     with the holders of the Common Stock and the Class A Common Stock, on all
     matters submitted to a vote of the holders of Common Stock or Class A
     Common Stock, in person or by proxy, in the same manner and with the same
     effect as the holders of Common Stock and Class A Common Stock; provided
     that the holders of Class B Common Stock and Class C Common Stock shall
     have no voting rights with respect to matters reserved (by law or by
     agreement with the Corporation) solely for any other class of capital
     stock.



                                       5
<PAGE>

               3.  Conversion.  (a)  Five business days after final
     determination of the Corporation's 1995 EBITDA and the Corporation's 1995
     Net Income in accordance with Subsection (c) below, the Class B Common
     Stock and Class C Common Stock automatically shall be converted as set
     forth in subsection (e) below.

               (b) No later than March 31, 1996, the Corporation shall furnish
     to TMC (i) copies of the audited consolidated financial statements of the
     Corporation for the calendar year 1995 (the "Corporation's 1995
     Financials") which are to be prepared in accordance with United States
     generally accepted accounting principals consistently applied ("GAAP") and
     accompanied by the unqualified opinion of the Corporation's auditors, and
     (ii) a certificate from the Corporation attested to by the Corporation's
     auditors calculating the Corporation's 1995 EBITDA and the Corporation's
     1995 Net Income. A copy of the certificate referred to in (ii) above shall
     be filed in the minute book of the Corporation.

               (c) The "Corporation's 1995 EBITDA" shall be equal to the
     Corporation's earning before interest, taxes, depreciation and amortization
     (as determined in accordance with GAAP), as set forth in the Corporation's
     1995 Financials, as adjusted as provided in this subsection (c) and the
     "Corporation's 1995 Net Income" shall be equal to the Corporation's net
     income (as determined in accordance with GAAP), as set forth in the
     Corporation's 1995 Financials, as adjusted as provided in this subsection
     (c).  In calculating the Corporation's 1995 EBITDA and the Corporation's
     1995 Net Income, all items of expense shall be included.  Notwithstanding
     the foregoing, in calculating the Corporation's 1995 EBITDA and the
     Corporation's 1995 Net Income, (a) any write-ups or write-downs of
     inventory (which shall be determined based on the lower of cost or market
     value of the Corporation's raw materials, work in process, supplies used in
     operations and finished goods, determined based on a last in, first out
     (LIFO) basis), based on changes in the market prices of petroleum
     feedstocks, blendstocks and refined products, (b) any nonrecurring events
     which accrue profit to the Corporation (e.g., settlements of litigation),
     (c) any gains or losses in the Corporation's portfolio of investment
     securities, (d) any book loss (which does not affect cash flow) on the
     Corporation's diesel desulfurizer, (e) EBITDA and Net Income of any
     entities acquired by the Corporation after February 27, 1995 (unless a
     binding acquisition agreement relating thereto shall have been entered into
     prior to such date), and (f) any items which artificially inflate EBITDA or
     Net Income for calendar year 1995, shall be disregarded.  In determining
     the "Corporation's 1995 EBITDA" and the "Corporation's 1995 Net Income"
     1995 turnaround expenditures in excess of $4,000,000 shall be expensed
     rather than

                                       6
<PAGE>

     capitalized, and such amounts in excess of $4,000,000 which are
     expensed shall not be amortized.

               (d) Auditors selected by TMC shall have the right to review the
     determination of the Corporation's 1995 EBITDA and the Corporation's 1995
     Net Income (including a review of accountants' working papers).  Any
     disputes relating to such calculation shall be finally determined by
     auditors selected jointly by the other two auditing firms.  Each of the
     three auditors described in this Section shall be a "Big Six" accounting
     firm and the cost of its services shall be paid by the Corporation.

               (e) Five days after the Corporation's 1995 EBITDA and the
     Corporation's 1995 Net Income are finally determined as provided for in
     subsection (c) and (d) above (the "Conversion Date"), each share of the
     Class B Common Stock and the Class C Common Stock shall be subject to a
     mandatory conversion into the number of shares of Common Stock and the
     number of shares of Class A Common Stock respectively as set forth under
     the Applicable Conversion Level.  The "Applicable Conversion Level" shall
     be the conversion level set forth in the chart below (EBITDA and Net Income
     numbers being expressed in millions of U.S. dollars) for the lower of the
     Corporation's 1995 EBITDA or the Corporation's 1995 Net Income (e.g., if
     the Corporation's 1995 EBITDA is 160 (conversion level 2) and the
     Corporation's 1995 Net Income is 47 (conversion level 4), the "Applicable
     Conversion Level" will be conversion level 2).

                                       7
<PAGE>

<TABLE>
<CAPTION>
-----------------------------------------------------------------------------------
                                              Conversion     Conversion
                                    AND          Ratio          Ratio
                   If               Net      per share of   per share of
 Conversion      EBITDA           Income     Class B into      Class C     Share
    Level          is:              is:        shares of     into shares   Price
                                                Common       of Class A
---------------------------------------------------------------------------------
<S>        <C>              <C>              <C>          <C>             <C>
      1       less than 158    less than 32       0.0            2.0       $13.33
---------------------------------------------------------------------------------
      2             158-169           32-38       0.4            1.6       $13.64
---------------------------------------------------------------------------------
      3             170-181           39-46       0.8            1.2       $13.95
---------------------------------------------------------------------------------
      4             182-193           47-53       1.2            0.8       $14.29
---------------------------------------------------------------------------------
      5             194-205           54-60       1.6            0.4       $14.63
---------------------------------------------------------------------------------
      6    greater than 205 greater than 60       2.0            0.0       $15.00
---------------------------------------------------------------------------------
</TABLE>

               4. Anti-Dilution. The Corporation shall not take any action
     (including, without limitation, payment of a dividend or distribution on
     the capital stock, subdividing or reclassifying any outstanding shares of
     capital stock, issuing capital stock at less than its book value, a merger
     or consolidation, or any other action) which may have the effect of
     diluting the value Class C Common Stock (or the Class A Common Stock into
     which the Class C Common Stock is convertible or the Common Stock into
     which such Class A Common Stock is convertible), except with the prior
     written consent of TMC (which consent shall not be unreasonably withheld so
     long as TMC is satisfied that appropriate anti-dilution protection and
     adjustments have been put into effect by the Company with respect to such
     capital stock).

               5.  Liquidation, Dissolution or Winding Up.  In the event of any
     Liquidation prior to the Conversion Date, for purposes of distributing the
     Liquidation Proceeds, each share of the Class C Common Stock is to be
     assumed to have been automatically converted into Class A Common Stock at a
     ratio of one share of Class C Common Stock to two shares of Class A Common
     Stock and the holders of Class C Common Stock shall be entitled to share on
     such basis, with the holders of Common Stock and Class A Common Stock, in
     the Liquidation Proceeds.

          E.  Amendment of this Article.  The Corporation may not amend, alter,
     change or repeal in any manner adverse to the holders of the Class A Common
     Stock or the Class C Common Stock the rights or preferences of the holders
     of the Class A Common Stock or Class C Common Stock contained in this
     Article 4 without the consent of the holders of 95% of the Class A Common
     Stock or Class C Common Stock, as the case may be.

                                       8
<PAGE>

          FOURTH:  That such amendment has been duly adopted in accordance with
the provisions of the General Corporation Law of the State of Delaware by the
unanimous written consent of the holders of all outstanding shares entitled to
vote thereon in accordance with the provisions of Section 228 of the General
Corporation Law.

          IN WITNESS WHEREOF, we have signed this certificate this 24th day of
February, 1995.


                                         CLARK USA, INC.



                                         By:  /s/  Paul D. Melnuk
                                            -----------------------
                                                 Paul D. Melnuk
                                                 President and
                                            Chief Executive Officer
ATTEST:


/s/  Patrick F. Heider
---------------------------
     Patrick F. Heider
        Secretary

                                       9