Marquis Teague and Trahson Burrell had boarded a plane on Christmas Eve en route to a game, however prior to take off a flight attendant claimed the men had taken blankets from the first class cabin.
The pair were subsequently forced off the plane. But it later emerged that they had been given the blankets by passengers.
Neither of the athletes has commented on the incident, but their team coach tweeted he believed the incident was driven by race.
Both of the basketball players are African American, as was the flight attendant involved.
A spokesperson for American Airlines said the carrier was now reviewing the incident. "We apologise for what occurred on this flight. We take pride in bringing people together, and we know that on this flight we let some of our customers down," he said.
The carrier has been attempting to address accusations of bias in the way it has treated some customers, the BBC reports.
The civil rights group NAACP warned in October of "a pattern of disturbing incidents reported by African-American passengers, specific to American Airlines".
American Airlines later pledged to put its 120,000 employees through new training.