U.S. and Canadian officials saved the weekend travel plans of about 3,000 bargain-seeking Air Canada passengers late yesterday by agreeing to start negotiations on a prickly international airline route and fare issue that has gone unresolved for more than two years.

The agreement temporarily set aside President Reagan's disapproval on Thursday of cut-rate tickets that Air Canada had already sold to thousands of passengers for weekend flights between Canada and many U.S. cities. Reagan was affirming a decision of the U.S. Civil Aeronautics Board.

Passengers who had taken advantage of Air Canada's "Transborder Seat Sale" discovered that the fine print on their tickets, "Pending government approval," actually meant something this time.

It wasn't until late in the day that the agreement was struck and the CAB ban was lifted. About 1,000 of the seats sold for this weekend at prices as much as 75 percent below regular coach fares were purchased by U.S. residents flying to Canada, an Air Canada spokesman said.

The agreement to negotiate protects only flights this weekend, and the return trips. The Transborder Seat Sale is to run on weekends through June 20, for which additional approval will be required.

U.S. officials would not say for attribution that future approval is contingent on progress in the negotiations, but confirmed this is so. The negotiations are scheduled to begin Monday.

This is the latest in a series of fractious issues between the two countries. Just this week, U.S. and Canadian scientists were unable to agree on the causes and effects of acid rain, which Canadians contend comes largely from coal-fired power plants in the United States.

The U.S. Justice Department this week labeled three Canadian films "political propaganda" and declared they could not be shown in the United States without a disclaimer that the U.S. government does not approve of them.

Earlier this year a moratorium was declared, then lifted, on granting permits for Canadian trucking firms to operate in the United States. And early this month the Commerce Department ruled the Canadian government had provided subsidies to a Quebec corporation that won a contract to build subway cars for New York City.

Air Canada's Transborder Seat Sale became the pawn in a long-running dispute concerning flights between Canada and Australia. Since April, 1980, Continental Air Lines, an American carrier, has sought Canadian approval of fares between Canada and the South Pacific that match the Canada-South Pacific fares of C P Air, a Canadian airline. Because its flights are through Honolulu, C P Air needs--and already has--U.S. approval for those fares.

Continental wanted to match the fares in an arrangement with either Western Airlines or Air Canada under which passengers would transfer to Continental in Los Angeles.

Repeated applications to Canada were rejected, according to U.S. officials. Thus, when Air Canada sought approval for its seat sale, an interagency U.S. group including the State and Transportation departments and the CAB agreed that this was the place to make a stand, an official said.

On Feb. 9 the Canadians were informed through diplomatic channels that the U.S. "herewith expresses dissatisfaction with Air Canada's proposed 'Seat Sale' fares." CAB Chairman Clinton D. McKinnon said that the Canadians were also told, "We'll sit down if you want to have negotiations leading up to matching of the fares" on the South Pacific routes.

Darrell M. Trent, deputy transportation secretary, said approval for flights this weekend came because of "an expression of good faith by Canada to help solve the problem."