U.S. District Judge David Doty also declined the NFL's motion that he recuse himself from the case. The league had accused him of bias.
Doty had ruled in February that the Falcons would violate the NFL collective bargaining agreement if they tried to recover the roster bonus money Vick already received.
Vick is serving a 23-month prison sentence after pleading guilty to federal charges in a dogfighting operation. After the plea, the Falcons tried to recover about $20 million in bonuses Vick earned from 2004 to 2007. A court-appointed expert concluded last October that the Falcons were entitled to recover the bonuses, but Doty disagreed, saying the team could only recover his signing bonuses.
Doty had jurisdiction over the case because he has long handled matters arising from the NFL's collective bargaining agreement with its players and has developed special expertise along the way. In his 15-page ruling Tuesday, he wrote that the NFL had failed to meet the "high bar" necessary to get a judge disqualified.