The four-year-old complaint alleged that the studio's exclusive licensing agreement with the sport's governing body "constituted an illegal monopoly", but EA has emerged relatively unscathed, Kotaku reports.
Customers who bought an American football game by EA Sports after 2005 are entitled to a small refund of $1.95 for Xbox 360, PlayStation 3 and Wii titles, or $6.79 for PlayStation 2, GameCube and Xbox purchases.
EA Sports has been hit with a five-year ban on any exclusive licensing deals with the NCAA after its current contract expires in 2014, but it is free to strike up a non-exclusive agreement.
The company's exclusivity agreement with the NFL, which brought an end to the NFL 2K series, was the primary target of the lawsuit, but both parties are free to continue under the same terms.
EA also agreed not to enter any exclusive arrangements with the Arena Football League for five years, but there has not been an official AFL game released in five years.
Watch a trailer for EA Sports' Madden NFL 12 below: