In explaining the decision via a letter, Goodell wrote, "Because protecting the integrity of the game is the Commissioner's most important responsibility, I decline to rewrite our Collective Bargaining Agreement to abrogate my authority and 'discretion' to hear 'any appeal' in a conduct detrimental proceeding."
The decision was widely expected. Two weeks ago, attorneys for Goodell had formally recommended that he reject the NFLPA's request that he step aside as arbitrator.
At the NFL's spring meetings in San Francisco on May 20, Goodell said that he looked forward to hearing "directly from Tom if there is new information or there is information that can be helpful to us in getting this right." Goodell had cited his role as arbitrator as part of a "long-established" process.
The NFLPA's motion asking Goodell to recuse himself cited "a process that has contained procedural violations of our collective bargaining agreement." The union called Goodell a "central witness in the appeal hearing," adding that he is not impartial. The NFLPA wanted a neutral party to serve as an arbitrator.
In his letter to the NFLPA explaining his decision, Goodell wrote, "Based on the unambiguous language and structure of the CBA, as well as common sense, I conclude that none of the arguments advanced by the NFLPA has merit."
Goodell disagreed with the NFLPA's stance that he could not serve as arbitrator because the discipline letter sent to Brady was signed by NFL executive vice president Troy Vincent.
"The identity of the person who signed the disciplinary letter is irrelevant," he wrote. "The signatory's identity does not influence in any way my evaluation of the issues; any suggestion to the contrary defies common sense."
Goodell also disagreed with the NFLPA's view that he may be a "necessary" and/or "central" witness in the appeal hearing.
"I am not a necessary or even an appropriate witness, much less a 'central witness' as the NFLPA contends," Goodell wrote. "I do not have any firsthand knowledge of any of the events at issue."
On the NFLPA's claim that he has "prejudged" the situation, Goodell wrote, "I reject it" and cited the long-standing role of the commissioner as arbitrator in disciplinary hearings. He added that while he appreciated the work of attorney Ted Wells to produce the Wells report into Deflategate, "That does not mean that I am wedded to their conclusions or to their assessment of the facts. Nor does it mean that, after considering the evidence and argument presented during the appeal, I may not reach a different conclusion about Mr. Brady's conduct or the discipline imposed. That is true even though the initial discipline decision was reached after extensive discussion and in reliance on the critical importance of protecting the integrity of the game. As I have said publicly, I very much look forward to hearing from Mr. Brady and to considering any new information or evidence that he may bring to my attention. My mind is open; there has been no 'prejudgment' and no bias that warrants recusal."
Brady was suspended last month for the first four games of the 2015 season for his role in the use of underinflated footballs in the AFC Championship Game in January. The Patriots also were fined $1 million and stripped of two draft picks -- a first-rounder in 2016 and a fourth-rounder in 2017.
Patriots owner Robert Kraft said last month he will not appeal those penalties.
Brady has hired attorney Jeffrey Kessler, who has taken on the league in a variety of other cases throughout the years, and could take Brady's case to court should his punishment not be reduced after appeal.