During the 2011 NFL season, Ninkovich recorded his first NFL touchdown when he intercepted a pass from New York Jets quarterback Mark Sanchez and returned it 12 yards for the touchdown. He also had another interception earlier in the same game when he caught a pass tipped by Jerod Mayo. Ninkovich had the best statistical season of his career, recording 74 tackles, 6.5 sacks, 2 interceptions (1 returned for a touchdown), 1 forced fumble, and 3 recovered fumbles while starting all 16 regular-season games. During the Patriots' 2011–2012 playoff run, Ninkovich recorded 5 tackles, 1.5 sacks, 1 tackle for a loss, and 2 quarterback hits against the Broncos during the Divisional Playoff game. Ninkovich also recorded seven tackles against the Ravens during the second round Conference Championship Game. On February 5, 2012, Ninkovich played in Super Bowl XLVI against the New York Giants at Lucas Oil Stadium in Indianapolis, Indiana, but the Patriots lost the Super Bowl to the Giants, 21-17. Ninkovich recorded 4 tackles (3 solo), 0.5 sacks, and 2 quarterback hits in the game.