On February 5, 2017, Ninkovich was part of the Patriots team that won Super Bowl LI. In the game, he had two assisted tackles as the Patriots defeated the Atlanta Falcons by a score of 34–28 in overtime. In a postgame interview with WBZ Sports, Ninkovich claimed the Patriots "broke down" in the locker room at halftime, resolving afterwards to play "one heck of a 30-minute half." The Patriots trailed 28–3 in the third quarter, but rallied all the way back to win the game 34-28 against the Atlanta Falcons. The game was the first to go to overtime, and the Patriots made the largest comeback in Super Bowl history.