The Senate last night approved a $2.1 billion supplement to this year's appropriation after Sen. John Stennis (D-Miss.) won a direct confrontation with the Carter administration over U.S. acquisition of naval destroyers originally ordered by the shah of Iran.

The supplemental appropriation authorization approved by 77 to 12, includes $265 million for accelerated development of a new and controversial intercontinental ballistic missile, known as MX.

The bill also authorizes the Navy to begin refurbishing its Forrestal-class aircraft carriers. In a stunning defeat for Virginia's two senators, the Senate voted to have that work performed at Philadelphia Naval Shipyard instead of by the Newport News (Va.) Ship and Drydock Co., which the Navy had favored.

That decision will cost Newport News 2,500 to 3,000 jobs plus substantial residual benefits for its local economy, if it is eventually sustained by both houses.

The fight over the shah's destroyers infuriated Stennis, to the dismay of Carter administration officials who are anxious to cultivate the Mississippi Democrat, particularly for the forthcoming debate on the strategic arms limitation treaty.

Stennis, chairman of the Armed Service Committee, indicated his belief that he had an understanding with the administration to support U.S. acquisition of four Spruance-class destroyers under construction in his home state at the Ingalls' Shipbuilding Co. in Pascagoula. Ingalls is a division of Litton Industries.

But today the administration lined up with Sen. Donald W. Riegle Jr. (D-Mich.), who offered an amendment striking authorization for two of the four ships from this defense bill.

Stennis cited testimony from Navy officials and a letter from Defense Secretary Harold Brown which he said showed their support for his plan to authorize the United States to buy all four destroyers originally ordered by Iran during the present fiscal year.

But Riegle cited other administration statements to the effect that two destroyers should be bought this year, two more in fiscal 1980. John White, a deputy director of the Office of Management and Budget, wrote to Riegle yesterday saying that was the definitive administration position.

"This is a repudiation of what everbody has told me," Stennis shouted on the floor. His senior colleague on Armed Services, Henry M. Jackson (D-Wash), spoke in Stennis's support, saying: "I've been around here a few years, and I've never seen such an amateurish operation" as the administration's on this issue.

In earlier debates Riegle has charged that buying the four destroyers is a bailout for Litton and Stennis's home state. The Navy has countered that it can make good use of the ships and save a lot of money by buying them, compared to prices for comparable new ships today.

When the Senate voted yesterday, Stennis came out the winner, 56 to 32. However, the House has authorized acquisition of only two of the Iranian destroyers this year, and a conference will have to work out a compromise.

The vote to refurbish the Saratoga-and presumably three other carriers that will be overhauled later-in Philadelphia will apparently cost the tax-payers more money but also aid an area suffering from high unemployment in the Northeast. A coalition of Northern senators, liberal Democrats and personal friends of the Pennsylvania, New Jersey and Delaware senators who pushed for Philadelphia won the day. The closest vote was 50 to 41 against a motion to kill by tabling the Philadelphia proposal.