"The codesharing relationships between American and these carriers no longer make sense to us", the Fort Worth, Texas-based company said. They claim the airlines rapid expansion in the U.S.is hurting American jobs.
"We are committed to the USA market and American consumers, and are taking all possible measures to ensure that the flying public is not harmed by this decision".
Canoll added that "there will likely be no economic ramifications for his insults" because Qatar Airways is funded by the Qatar government, and doesn't have to compete in the free market like other airlines.
The break-up comes as US carriers, including American, have been urging the USA government to take action against three Middle Eastern carriers - Etihad, Qatar and Emirates - alleged to have received billions of dollars in subsidies from their home governments.
"We view the decision by American Airlines as being anti-competitive and anti-consumer".
Qatar Airways CEO Akbar Al Baker is apologising for referring to United States airline flight attendants as "grandmothers".
Mr Al Baker said he was disappointed with the decision but said he would continue with plans to buy a 10% stake in American Airlines. The move came one week after Qatar announced that it would attempt to acquire up to a 10% share of American stock, prompting objections from American CEO Doug Parker.
For the past two years, American, Delta Air Lines and United Airlines have urged the US government to renegotiate Open Skies agreements with Qatar and the United Arab Emirates, alleging that Qatar, Etihad and Emirates airlines have received more than $42 billion in government subsidies and loans. "This action will reduce choices for consumers and may result in higher fares for travelers to and from the United States".
But on Wednesday, Al Baker walked back his statements, calling them "careless".
However, American's decision to end the codeshare agreement with Etihad and Qatar doesn't mean an end to their business relationship.
"American Airlines continues to believe that the [US] president and his administration will stand up to foreign governments to end massive carrier subsidies that threaten the U.S. aviation industry and that threatens American jobs", the company said in a filing.