"It was right here. I know exactly where I put it," Brady said as he called the security staff and team equipment managers to assist in the search.
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Brady, who was named the Super Bowl MVP for the record fourth time in his career, frantically looked through several bags and told nearby players that the iconic No. 12 was missing.
Backup quarterback Jimmy Garoppolo told other players to look for the jersey, but the longer he searched, the more Brady seemed to grow concerned it had been stolen.
"This is not good," he said. "It was right here and now I don't have it. Not good."
While walking out of the stadium, Brady was asked by USA TODAY Sports if he had managed to locate the jersey during his extensive search.
"No," he replied. "It is going to be on eBay soon, I guess."
Follow Martin Rogers on Twitter @mrogersUSAT.