Federal Aviation Administration officials said yesterday they will withdraw a proposed rule that was vigorously opposed by the Air Line Pilots Association, but the move was not enough to save the job of longtime ALPA President John J. O'Donnell.

The proposed rule, generally supported by the airlines, would have relaxed present limits on flight and duty time for pilots. Among other things, the rule would have removed an annual ceiling on cockpit hours and increased the limits on how many hours a pilot legally can fly within a week.

The ALPA had charged the proposal "will substantially increase pilot fatigue and lead to significant reductions in aviation safety."

News that the FAA was planning to withdraw the proposal came the same day the ALPA board of directors was choosing a new president in Miami. Henry A. (Hank) Duffy, chairman of the Delta Airlines pilot group, was elected to replace O'Donnell, who has held the job since 1971.

O'Donnell has been on unusually friendly terms with the Reagan White House. Further, Robert Bonitati, a special assistant to the president who specializes in labor matters, was a lobbyist for ALPA before taking his White House job.

Transportation Secretary Drew Lewis spoke at the ALPA meeting Tuesday in what was widely regarded as a show of support for O'Donnell and said the department would be modifying the proposed flight time rule.

FAA spokesman Ed Pinto confirmed the proposal will be withdrawn, but denied the action had anything to do with ALPA politics. "There have been a huge number of comments on the proposal," Pinto said, "and the people who do these things decided they needed to take another look."

ALPA sources said Duffy's victory was a surprise but there was no single issue dividing Duffy or O'Donnell. "It's just a tough time to be a union leader," one source said.

Cut-rate airlines are paying nonunion pilots as little as $30,000 a year and significantly undercutting major carriers, who have to pay as much as $150,000 for some ALPA jobs. In the last two years, the ALPA has lost an attempt to force a regulation requiring three-person cockpits in new jetliners and a battle to get Congress to require labor protection plans in the event of airline mergers or acquisitions.