<PAGE>

                                                                     Exhibit 3.3


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


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

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

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


          I, Maura Clark, Executive Vice President 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 Restated Certificate of Incorporation of the
Corporation was filed by the Secretary of State of the State of Delaware on the
28th day of December, 1994.
          SECOND:  That Article 4 of the Certificate of Incorporation of the
Corporation has been amended to read in its entirety as follows:

               ARTICLE 4.  The total number of shares of capital stock which the
     Corporation shall have the authority to issue is 59,554,552 shares
     consisting of (a) 54,554,552 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 (v) 3,389,955 shares
     shall be designated "Class D Common Stock"; and (b) 5,000,000 shares of
     "Preferred Stock," par value $.01 per share.
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     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 Classes, 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 Common Stock shall be entitled to receive, when,
as 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 share of Common Stock shall entitle the holder thereof
to one vote, voting together with the holders of 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 (a "Liquidation"), 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
and Class C Common Stock shall be entitled, the holders of all outstanding
shares of Common Stock shall be entitled to share ratably, on a share-for-share
basis, with the holders of Class A Common Stock, Class C Common Stock and Class
D Common Stock in the remaining assets of the Corporation.

     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, the Class B Common Stock, the Class C Common Stock or the Class D
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 unless the
same

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<PAGE>

dividend or distribution per share has been declared or paid, as the case
may be, with respect to the Common Stock, the Class B Common Stock, the Class C
Common Stock and the Class D Common Stock.  Any cash dividend paid on the Class
A Common Stock 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 and 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).

          5.  Liquidation, Dissolution or Winding Up.  (a)  In the event of
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, on a share-for-share basis, with the holders of Common Stock, Class D
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,
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

                                       3

<PAGE>

below in connection with the Class C Common Stock) and Class D 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) 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 and Class D Common Stock shall share ratably, on a share-
for-share basis, 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, on a share-for-share basis, with the holders of Common Stock, Class D
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 TMC, affiliates of TMC, The Horsham
Corporation ("Horsham"), affiliates of Horsham and employees of the Corporation
exceeds $150 million.

          "Purchase Price" means (a) if the Liquidation occurs prior to the
Conversion Date (as defined below), $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, the Class A Common Stock or the Class D
Common Stock, and the Board of Directors may not declare or pay any dividend or
distribution with respect to the Class B Common Stock or the Class C Common
Stock unless the same dividend or distribution per share has been declared or
paid, as the case may be, with respect to the Common Stock, the Class A Common
Stock and Class D Common Stock.  Any cash dividend paid on the Class B Common
Stock or the Class C Common Stock 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.

                                       4
<PAGE>

          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 share 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.

          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 shall automatically 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
principles 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, the following
shall be disregarded:  (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

                                       5

<PAGE>

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. 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 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 calculations 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 Class C Common Stock shall be converted into the number of
shares of Common Stock and the number of shares of Class A Common Stock,
respectively, as set forth in the chart below for 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).

                                       6
<PAGE>

<TABLE>
<CAPTION>
---------------------------------------------------------------------------------------
                                               Conversion     Conversion
                                     AND          Ratio          Ratio
                    If               Net      per share of   per share of      Share
Conversion        EBITDA            Income    Class B into      Class C        Price
  Level            is:               is:       shares of     into shares
                                                 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 shall be assumed to
have been automatically converted into shares of 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.  Class D Common Stock

          1.  Dividends.  Subject to the preferential rights, if any, of the
Preferred Stock, the holders of Class D 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, the Class A Common Stock, the Class B Common Stock and the Class C
Common Stock, and the Board of Directors may not declare or pay any dividend or
distribution with respect to Class D Common Stock unless the same dividend or
distribution per share has been declared or paid, as the case may be, with
respect to the Class A Common Stock, the Class B Common Stock and the Class C
Common Stock.  Any cash

                                       7
<PAGE>

dividend paid on the Class D Common Stock shall be paid in immediately available
funds in such manner as the holders of Class D Common Stock shall reasonably
request.

          2.  Voting Rights.  Holders of shares of Class D Common Stock shall
not be accorded any voting rights in respect thereof and such shares shall not
be deemed to be outstanding for purposes of determining the vote required on any
matter properly brought before the stockholders of the Corporation for a vote
thereon.

          3.  Conversion.  (a)  The Company shall have the right, at any time
and from time to time, to convert any or all of the shares of Class D Common
Stock into an equal number of shares of Common Stock.  The method of selection
of such shares shall be determined by the Board of Directors of the Company in
its sole discretion.

          (b) Following an initial public offering of Common Stock, any person
who is not an affiliate of Occidental Petroleum Corporation to whom shares of
Class D Common Stock have been directly or indirectly transferred by Occidental
Petroleum Corporation in an arm's-length transaction shall have the right, at
any time and from time to time, to convert any or all of such shares of Class D
Common Stock into an equal number of shares of Common Stock.

          (c) Following an initial public offering of Common Stock, any person
who is not an affiliate of Gulf Resources Corporation to whom shares of Class D
Common Stock have been directly or indirectly transferred by Gulf Resources
Corporation in an arms-length transaction shall have the right, at any time and
from time to time, to convert any or all of such shares of Class D Common Stock
into an equal number of shares of Common Stock.

          4.  Liquidation, Dissolution or Winding Up.  In the event of any
Liquidation, 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 and Class C Common Stock
shall be entitled, the holders of all outstanding shares of Class D Common Stock
shall be entitled to share ratably, on a share-for-share basis, with the holders
of Common Stock, Class A Common Stock and Class C Common Stock in the remaining
assets of the Corporation.

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<PAGE>

          5.  Anti-Dilution.  In the event the Company shall at any time (a)
declare a dividend on any shares of capital stock of the Company or any
securities issued in respect thereof, or in substitution therefor, in connection
with any stock split, dividend or combination, or any recapitalization, merger,
consolidation, exchange or other similar reorganization (a "Recapitalization"),
such dividend being payable in shares of capital stock of the Company, (b)
subdivide the outstanding capital stock of the Company, (c) combine the
outstanding capital stock of the Company into a smaller number of shares, or (d)
issue any shares of capital stock in a Recapitalization, the number of shares of
Class D Common Stock then outstanding shall be proportionately adjusted so that
the relative equity percentage ownership of the Company and the relative voting
power represented by each such share shall be preserved as nearly as
practicable.

     F.  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 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.

          THIRD:  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.

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<PAGE>

     IN WITNESS WHEREOF, I have signed this certificate this 2nd day of
November, 1995.

                                   CLARK USA, INC.



                                   By:  /s/  Maura Clark
                                      -------------------------
                                       Maura Clark
                                       Executive Vice President

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