Brady fought his four-game suspension that NFL Commissioner Roger Goodell imposed after the "deflategate" scandal stemming from last season's playoff game.
Federal judge Richard Berman said he vacated Goodell's decision, in part, because it was "premised upon several significant legal deficiencies, including (A) inadequate notice to Brady of both his potential discipline (four-game suspension) and his alleged misconduct; (B) denial of the opportunity for Brady to examine one of two lead investigators, namely NFL Executive Vice President and General Counsel Jeff Pash; and (C) denial of equal access to investigative files, including witness interview notes."
The NFL said it "respectfully" disagrees, and later in the day filed court papers indicating that it intends to appeal Berman's ruling.
"The commissioner’s responsibility to secure the competitive fairness of our game is a paramount principle, and the league and our 32 clubs will continue to pursue a path to that end," the NFL said in a statement today. "While the legal phase of this process continues, we look forward to focusing on football and the opening of the regular season."
Both sides -- Brady and the NFL Players Association in one corner and the NFL and Goodell in the other -- had failed to reach a settlement. Patriots fans had been awaiting the judge's ruling with bated breath before the team's first game of the season on Sept. 10 against the Pittsburgh Steelers.
Berman said Brady's punishment "cannot reasonably" be the equivalent of the four-game suspension handed down to players who use steroids, as noted in the collective bargaining agreement with players. In the latter case, the policy details testing procedures, an appeal right, discovery process, and burdens and standards of proof.
"Brady also had no notice that his discipline would be the equivalent of the discipline imposed upon a player who used performance enhancing drugs," Berman wrote.
The case raised questions about the arbitration process within the NFL. While the NFL asked the judge to affirm Goodell's broad authority to protect the integrity of the game, the union argued that there are limits to the commissioner's authority under the collective bargaining agreement. Berman made no determination whether Brady actually tampered with footballs.
Goodell's denial of Brady's motion to compel the testimony of Pash, co-lead investigator with attorney Ted Wells, was "fundamentally unfair," Berman wrote. NFL arbitration precedent says players must be afforded the opportunity to confront their investigators, Berman noted.
Wells declined to comment to ABC News.
The NFL Players Association said in a statement that today’s decision “should signal to every NFL owner that collective bargaining is better than legal losses.”
“This decision should prove, once and for all, that our Collective Bargaining Agreement does not grant this Commissioner the authority to be unfair, arbitrary and misleading,” the NFL Players Association said in a statement today. “While the CBA grants the person who occupies the position of Commissioner the ability to judiciously and fairly exercise the designated power of that position, the union did not agree to attempts to unfairly, illegally exercise that power, contrary to what the NFL has repeatedly and wrongfully claimed."
Brady's suspension was first handed down in May, along with a $1 million fine levied on the New England Patriots and the loss of the club's first-round selection in the 2016 draft and fourth-round in the 2017 draft. Brady's suspension was then upheld by the NFL in July. The punishment revolves around the deflation of footballs used during the AFC Championship game against the Indianapolis Colts on Jan. 18. The Patriots won that game 45-7, then went on to win the Super Bowl on Feb. 1 against the Seattle Seahawks.
Brady has denied the allegation.
"I did nothing wrong, and no one in the Patriots organization did either," Brady wrote in a Facebook post in July.
Patriots owner Robert Kraft said he regrets not taking legal action in May when the team was first fined by the NFL.
"I was wrong to put my faith in the league," Kraft said during a news conference in July, adding that Brady "is a person of great integrity and is a great ambassador of the game both on and off the field."
Wells stated in May that it "is more than probable" that Brady "was at least generally aware of the inappropriate activities" involving the release of air from the Patriots' footballs.