The NFL players union, through the collective bargaining process, gave the league and its commissioner the power to discipline players for violations of league standards. The contract provides for a grievance process for players to challenge league rulings. The decision Thursday from federal Judge Richard M. Berman, in lifting the four-game suspension of New England Patriots quarterback Tom Brady, sends the message that the grievance process has to meet at least minimal standards of fairness.

In the case of Mr. Brady, it did not even come close.

It remains baffling why the NFL and Commissioner Roger Goodell, acting on scant evidence, chose to turn this relatively minor matter about the possible slight deflation of footballs into a massive controversy and, literally, a federal case.

On Thursday, the ball exploded in Mr. Goodell’s face. Judge Berman, who had made clear during hearings in his court that he did not see any evidence of Mr. Brady’s involvement in deflating footballs, ruled that the league did not adequately notify Mr. Brady of the potential discipline he faced; did not give him the chance to question a lead investigator; and denied the quarterback the chance to access the investigative files.

The commissioner, Judge Berman concluded, had wrongfully “dispensed his own brand of industrial justice.”

The ruling will place substantial limits on the commissioner’s power, ironic since the case itself had little to do with anything of substance. The allegation is that to gain an advantage, a game-day employee of the Patriots slipped into a restroom and took some air out of the footballs that were used by Mr. Brady in the AFL championship game.

A recheck at halftime showed the air pressure in the footballs was below the 12.5-PSI minimum. Other studies concluded atmospheric conditions could have explained the pressure loss. In any event, they were re-inflated and Mr. Brady performed better in the second half in a 45-7 rout of the Indianapolis Colts.

The NFL’s multi-million-dollar investigation turned up no direct evidence of what happened in the restroom and no evidence at all of Mr. Brady’s participation in deflating footballs. Yet Commissioner Goodell somehow reached the conclusion, in upholding a four-game suspension, that the New England quarterback "knew about, approved of, consented to, and provided inducements and rewards" to ensure balls were deflated.

It was a baseless conclusion culminating an unfair process.

Rather than appeal, as it plans to, the NFL should reform its grievance procedures and pick its fights more carefully.