"The codesharing relationships between American and these carriers no longer make sense to us", the Fort Worth, Texas-based company said. The agreement was a way for airlines to book passengers on each other's flights.
Qatar Airways Chief Executive Akbar al-Baker said on Thursday he was disappointed by the decision, but it would not affect the Middle East carrier's plans to buy up to a 10 percent stake in American, announced last month.
For instance, this allows Qatar Airways to sell flights fly from Doha, Qatar to Charlotte, North Carolina by transferring its passenger to an American Airlines flight in Philadelphia or Chicago.
In its statement issued Wednesday, American said the ending of the codeshare pacts would not hurt it financially.
Qatar Airways' newest ambassador Fahad Al Qubaisi said: "I'm thrilled to be here for this important event, where we have gathered to show our unity as a nation in the midst of this blockade".
American said the decision to end the deals would have no material impact on its finances.
Baker and Qatar Airways have not responded to the massive condemnation.
His comments were labelled "insulting" and "sexist and ageist" by American Airlines and angered U.S. pilot groups and unions.
The US airline said it was making the move as "an extension of our stance against the illegal subsidies that these carriers receive from their governments".
Qatar Airways said last month it planned to take up to a 10% stake in the United States airline, a move that came as a surprise to the executives as the U.S. airline.
The controversy comes as American Airlines cancelled a codeshare agreement with both Qatar Airways and Etihad, accusing them of receiving unfair state subsidies.
The carrier plans to launch services to 25 new destination throughout 2017-2018, including to Canberra in Australia; Chiang Mai in Thailand; Las Vegas and San Francisco in the US; Rio de Janeiro in Brazil; and Santiago in Chile.