The website made the move to protest American pulling its flight information off a rival site, Orbitz, earlier this week.
Expedia said it “cannot support efforts that we believe are fundamentally bad for travelers.”
The changes on Expedia include moving American's flight options out of its prime spot on the first page of results. Instead of seeing prices immediately when searching, American's fares are now visible only after choosing both a departure and return flight.
Expedia said in a statement that it believes the airline's move to pull fares from Orbitz will result in higher ticket prices and make it harder for consumers to find deals.
But in a statement, American criticized Expedia’s move and hinted that it may file a lawsuit.
“This discriminatory action is unwarranted, especially considering that American has taken no action against and continues to operate in good faith with Expedia,” the statement said.
American pulled its flights from Orbitz on Tuesday in an intensifying dispute between airlines and online travel sites that sell its tickets.
Airlines have traditionally paid sellers a commission. American also pays fees to the global distribution companies that provide the flight information.
American wants Orbitz to get that flight information directly from the airline, cutting out the global distribution systems. American has said the move will reduce costs and also allow it to make more personalized offers to customers such as hotels and car rentals.
"American is trying to get rid of the middleman, which is ironic, because American created the middleman back in the '60s when they invented Sabre,” said Andrea Ahles, an aviation writer for the Fort Worth Star-Telegram.
Many travel agents -- both traditional and online -- want all the flight information from all the airlines side by side.
"American has the right to distribute its product however they want to,” said Terry Denton, president of Travel Leaders in Fort Worth. “Consumers inevitably are going to be limited in their choices because it's going to be more difficult for consumers to compare and contrast fares.”
Some experts say American underestimated Orbitz' role in the ticketing process. About a third of Americans book their tickets on independent travel sites.
"Online consumers may not even know American's flights are missing. The ones who will gain the most here are American's competitors -- United, Southwest and others," said Kevin Mitchell, chairman of the Business Travel Coalition, which represents corporate travel buyers.
Analysts predict more fireworks in the year ahead as a lawsuit between American and Orbitz winds its way through the courts.