The league also announced another jersey worn by Brady in Super Bowl XLIX in 2015 was retrieved after an investigation led by the FBI -- both found in possession of an international media member.
The jerseys were found in Mexico and are being authenticated by authorities, Houston Police Department Chief Art Acevedo said.
"Through the cooperation of the NFL and New England Patriots' security teams, the FBI and other law enforcement authorities, the Super Bowl LI jersey worn last month by MVP Tom Brady has been recovered," the NFL said in a statement. "Also retrieved during the ongoing investigation was the jersey Brady wore in the Patriots' victory in Super Bowl XLIX against the Seattle Seahawks in 2015.
"The items were found in the possession of a credentialed member of the international media. Due to the ongoing investigation, we would refer any additional questions to the FBI."
Brady discovered his latest jersey was missing following the Patriots' 34-28 overtime victory over the Atlanta Falcons in Super Bowl LI on Feb. 5.
"Someone stole my game jersey," Brady is seen telling Patriots owner Robert Kraft after the game at NRG Stadium in Houston.
"You better look online," Kraft joked.
"It's unfortunate, because that's a nice piece of memorabilia," Brady told the media the next day when he accepted the Super Bowl MVP trophy. "If it shows up on eBay or something, somebody let me know. I'll try to track that down. Those are pretty special ones to keep. But what can you do? I'll take the ring. That's good enough for me."
Kraft later compared the jersey to a piece of fine art.
"It's very sad to me that someone would do something like this, and it's like taking a great Chagall or Picasso or something. You can never display it," Kraft said last month.
The Houston police assigned a value of $500,000 to the jersey in its report. A Lelands auction house representative told the Boston Globe last month it could be worth as much as $1 million.
The jersey Brady wore in the Patriots' 28-24 victory in Super Bowl XLIX against the Seattle Seahawks in February 2015 was also retrieved during the investigation. It was not common knowledge that jersey was missing.
The 39-year-old Brady set Super Bowl records for most passing attempts (62), most completions (43) and most passing yards (466) as New England overcame a 28-3 deficit to beat the Falcons. He became the first quarterback to win five Super Bowls, and he tied Charles Haley for the record as a five-time Super Bowl champion.