The Air Force, which abolished the cost-cutting job of A. Ernest Fitzgerald after he revealed a $2 billion overrun in the C5A air transport program in 1968, has been ordered to reinstate him as deputy for management systems or equivalent status.

The reinstatement was decreed by U.S. District Court Judge William B. Bryant on Tuesday with an order that severely reprimanded former top officials of the Air Force for their "extraordinary . . . pressuring" of the old Civil Service Commission. He cited "threats" to have then-secretary of the Air Force John McLucas "contact" Robert Hampton, CSC chairman at the time, to have the commission endorse an Air Force denial that it had converted Fitzgerald into a figurehead while retaining his GS17 civil service rank.

At the Pentagon, Fitzgerald said, "I do hope the Air Force won't fight it any longer because I'd love to join in cost-cutting efforts on big accounts." The new Air Force secretary, Verne Orr, had no immediate comment. Bryant retained control of the case to assure that his order is obeyed.

The order followed more than a decade of battling by Fitzgerald in the CSC and the courts to over-come the Pentagon's determination -- in Democratic and Republican administration alike -- to keep him in a kind of limbo.

The Air Force dismissed Fitzgerald 11 years aog, claiming that a reduction-in-force had been dictated by budget cuts. Asserting that the dismissal was punishment for disclosing the C5A cost overrun in Senate testimony, he appeared to the CSC. In 1973 it ordered him restored to his old job.

McLucas, deciding to keep Fitzgerald away from major weapons system work until he could show that he was, in the words of Thomas Moran, a top aide to the secretary," a 'good' Air Force employe," assigned him to a newly created position, deputy for productivity management. Then began the efforts to persuade the CSC that its order had been carried out.

Fitzgerald, contending that the new post was "in no way comparable" to the old one, appealed again. Michael Sedmak, the CSC's chief appeals officer, ruled for the Air Force, but Bryant overturned his ruling in 1974.In a 1976 decision that Bryant termed arbitary and capricious, Sedmak ruled again for the Air Force.

In this week's ruling for Fitzgerald, Bryant said the Air Force had denied him the procedures required by law and that Sedmak's ruling lacked "any rational basis," being "unsupported by evidence in the record."