The decision from Berman said he voided the suspension in part because of "inadequate notice to Brady of both his potential discipline (four-game suspension) and his alleged misconduct."
The court also said it nullified the punishment because of "denial of the opportunity for Brady to examine one of two lead investigators"—NFL Executive Vice President and General Counsel Jeff Pash—and the "denial of equal access to investigative files, including witness interview notes."
The NFL denied Brady's appeal of the suspension in July, with Commissioner Roger Goodell charging that "important new information" helped firm up his decision.
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"Notwithstanding my enormous respect for his accomplishments on the field and for his contributions and role in the community, I find that, with respect to the game balls used in the AFC Championship Game and the subsequent investigation, Mr. Brady engaged in conduct detrimental to the integrity of, and public confidence in, the game of professional football," Goodell wrote in July.
Drew Rosenhaus, sports agent and CEO of Rosenhaus Sports, said he would not advocate for getting the decision overturned if he were advising the league.
"If I were them I would move on. This has been a disaster for the NFL, they've gone after one of their icons—why I'm not sure—to an extent they've marred the season, it's been an overriding story this off-season, it's really had a negative impact on the Super Bowl," he told CNBC.
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"Now it's a terrible embarrassment, it's a huge victory for Brady and the NFL Players Association, and it's absolutely something that will set a precedent—in my opinion—for other players going forward," Rosenhaus added.
The Thursday decision could even potential affect the NFL going forward.
Rosenhaus said Goodell and his management are "big losers here and there's a lot of egg on their face," especially as there's been significant financial and time investment in punishing Brady.
Brady has denied any involvement in the footballs' deflation from the start. In a January press conference, the quarterback admitted that "every team is trying to do the best they can to win every week," but that he was "as surprised as anybody" about the allegations.
In response to the judge's ruling, the NFL Players Association said in a statement that the "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."
"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," the statement added. "We are happy for the victory of the rule of law for our players and our fans."