Expedia moved American's flight options out of its prime spot on the first page of results in protest of the airline's decision to pull its flight information off a rival site, Orbitz, earlier this week.
"Expedia has chosen to no longer offer American Airlines fares on its website," American said in an statement posted on its website. "Customers looking to compare flights or fares online should visit other travel sites such as Kayak.com or Priceline.com for the most accurate and up-to-date information."
The Fort Worth, Texas-based airline has said that it would like to sell more tickets through its own website, as paying to have its flights listed on sites such as Expedia can be costly. Airlines have to pay a commission every time people search a particular flight, look up a fare or book a trip.
American, which is owned by AMR Corp., also claims it can offer more personalized packages such as hotel and flight deals to fliers who purchase tickets directly from the airline.
Expedia's removal of American flights marks an escalation in a months-long dispute between the airline and various travel sites. Last month, American Airlines pulled its flights from travel website Orbitz, saying consumers could just as easily buy tickets from American's website and "we won't have to pay as much for it."
Last week, Expedia made American flights more difficult to find on its website, an apparent response to the airline's decision to drop Orbitz. Expedia warned that it "cannot support efforts that we believe are fundamentally bad for travelers."
Experts have cautioned that while American might save money in commission fees, its sales will drop if its flights don't appear on travel sites such as Orbitz and Expedia. About a third of Americans book their tickets on independent travel sites.
Analysts have added that only smaller airlines such as Southwest Airlines Co. can get away with selling tickets exclusively on their own websites, as these airlines already have a reputation for offering cheap fares.
Bellevue, Wash.-based Expedia did not immediately respond to a message seeking comment on Saturday.