Pentagon whistle blower A. Ernest Fitzgerald, fired from the Air Force for revealing multibillion dollar cost overruns, won his 13-year legal battle for reinstatement yesterday.

Under a settlement agreement approved by U.S. District Court Judge William B. Bryant, Fitzgerald will resume his original duties and responsibilities, including review of the costs of major Air Force weapons and equipment purchases. He will not receive additional pay because he is already receiving the maximum allowable $57,500 salary.

The settlement also required the Air Force to pay Fitzgerald's lawyers $200,000 for their costs and expenses in the lengthy battle. Fitzgerald's chief lawyer, John Bodner Jr., told Bryant the lawyers would keep $8,000 of that payment to cover their costs and would donate the remaining $192,000 to legal services organizations.

Fitzgerald, 55, was fired from the Air Force in 1969, a year after he told Congress about $2 billion in cost overruns in the purchase of C5A military transports. In 1973 the Civil Service Commission ordered him reinstated with back pay, but Fitzgerald sued a year later, claiming that the job he was given was not the one he had before he exposed the overruns.

In a telephone interview yesterday, Fitzgerald said he was "glad to get back to doing what I was doing 13 years ago before I was so rudely interrupted." Fitzgerald said his present job as deputy for productivity management, while "certainly not completely useless," was "something an assistant of mine used to do."

He said he would have to take some time to catch up on his new job because he was cut off from his old duties when he "committed truth" in testifying about the overruns.

Under the settlement agreement, Fitzgerald said he would be management systems deputy to the assistant secretary of the Air Force for financial management, a job he said was "essentially the same job as I had before."

The Air Force is "glad to have this whole thing behind us," spokesman Col. Thomas G. Hanlin said yesterday. Hanlin said the suit was settled at the urging of Air Force Secretary Verne Orr.

Fitzgerald said Orr recently had indicated to him that "he wanted to see me back in action."

Fitzgerald said the 13-year "exile" from his job was difficult, and that he felt his experience had deterred potential whistle blowers from speaking out. "Nobody is going to get out and do what I did when they see what happened to me," he said.

"I'd do it differently if I had it to do over again," he added. "I would have had a job lined up and a lawyer ready. Others will never have the legal resources from the ACLU and the local law firm of Howrey & Simon that I had."

Fitzgerald claimed President Nixon fired him. In an action separate from the suit settled yesterday, he sued Nixon and aides Bryce Harlow and Alexander Butterfield for $3.5 million. That suit is still pending in the U.S. Supreme Court, which has agreed to decide whether Fitzgerald has the right to sue those officials over his firing. Nixon, Harlow and Butterfield have denied Fitzgerald's allegations.

In May 1980 Nixon agreed to pay Fitzgerald $142,000 on the condition that however the Supreme Court ruled, Fitzgerald would not take the former president through the public spectacle of a trial. Nixon and Fitzgerald also agreed that if the court ruled in Fitzgerald's favor, Nixon would pay him an additional $28,000.

In 1979, Fitzgerald's lawyers obtained transcripts of White House tape recordings that they claim show that Nixon fired Fitzgerald.

"I'd marked it in the news summary," Nixon told presidential aide Charles W. Colson, according to the transcript. "That's how that happened. I said get rid of that son of a bitch." Justice Department lawyers contended that the tapes did not prove that Nixon ordered Fitzgerald's ouster.

Nixon said at a press conference the same day he talked to Colson that he had ordered Fitzgerald fired but press secretary Ron Ziegler later told reporters Nixon had "misspoken."