The Senate Armed Services Committee has agreed, over Pentagon objections, to the most sweeping reorganization of the Joint Chiefs of Staff since the nation's top military body was created in 1947, informed sources said yesterday.

Committee Chairman Barry Goldwater (R-Ariz.), Sam Nunn (Ga.), the panel's ranking Democrat, and their allies prevailed over Sen. John W. Warner (R-Va.) and his supporters in a closed-door showdown on the issue Thursday, the sources said.

Pentagon officials who have been lobbying against the restructuring predicted yesterday that President Reagan would veto the measure if it remains in its current form. "The fight isn't over," one opponent said.

As approved by the Senate committee, the measure would centralize authority in the chairman of the Joint Chiefs, rather than limiting him to the role of mediator in inter-service disputes, and allow him to make his own recommendations to the president on military questions, rather than just giving the consensus view of the Army, Navy, Air Force and Marine Corps.

The Joint Chiefs of Staff now comprises a chairman, who can be from any of the services; the Army and Air Force chiefs of staff, the chief of naval operations and the Marine Corps commandant.

They meet as a corporate body and try to form a unanimous position on major military questions.

Under the current system, the heads of the services take turns filling in for the chairman when he is unavailable. In this role of acting chairman, which would be relinquished and filled by a deputy chairman under the measure just approved by the Senate panel, the service chief briefs the president and the secretary of defense on the latest military issues.

The measure calls for appointment of a deputy to the chairman of the Joint Chiefs who would outrank the heads of the military services in the decision-making process. The current chiefs object to this change, contending that the deputy could screen them off from top civilian policymakers.

In a concession to Warner, the committee added language to its draft that would give the service chiefs a direct channel to the president and the secretary of defense in the event the chiefs disagreed with recommendations made by the chairman or his deputy, sources said.

Defense Secretary Caspar W. Weinberger has contested the view of Goldwater and Nunn that the current system needs to be changed. Weinberger joined the chiefs in opposing the appointment of a deputy chairman.

An aide said last night that Weinberger will study the much-amended draft measure before deciding how to fight the next round as the bill heads to the Senate floor and is considered by the House.