An FBI-led investigation found both jerseys in Mexico and they are in the process of being authenticated by authorities.
Brady took the Super Bowl Most Valuable Player award in New England's 34-28 overtime victory over the Atlanta Falcons last month as well as the Patriots' 28-24 victory over Seattle in suburban Phoenix, Arizona, in 2015 when the previously unknown missing jerseys was taken.
An FBI-led investigation found both jerseys in Mexico and they are in the process of being authenticated by authorities, Houston Police Chief Art Acevedo said.
"The items were found in the possession of a credentialed member of the international media," the NFL announced in a statement.
"Through the cooperation of the NFL and New England Patriots' security teams, the FBI and other law enforcement authorities, the Super Bowl 51 jersey worn last month by MVP Tom Brady has been recovered.
"Also retrieved during the ongoing investigation was the jersey Brady wore in the Patriots' victory in Super Bowl 49 against the Seattle Seahawks in 2015."
Several media reports after the announcements identified the person who allegedly took the jerseys as Mauricio Ortega, a former executive with Mexico's Diario La Prensa.
Houston police had listed the Super Bowl 51 jersey, which was missing for six weeks, as worth $500,000.
The league said an FBI investigation was ongoing.
A video on the NFL's website showed Brady's shock at learning his jersey was missing.
"Someone stole my game jersey," Brady told Patriots owner Robert Kraft in the locker room after last month's Super Bowl, to which Kraft replied, "You better look online."
The morning after the game, Brady told the media: "The jersey, I put it in my bag and I came out and it wasn't there anymore. It's unfortunate because that's a nice piece of memorabilia. If it ends up on eBay, let me know. I'll try to track that down. Those are pretty special ones to keep."
Brady, 39, completed 43-of-62 passes for 466 yards -- all Super Bowl records -- in rallying the Patriots from a 28-3 deficit to defeat Atlanta, becoming the first quarterback to win five Super Bowls.