With Patriots driving for a winning score in the game's final minute, Thomas denied a potential touchdown pass by Tom Brady and then picked off the New England signal-caller with 2 seconds remaining, sealing the result.
The victory kept the Dolphins (8-6) in control of an AFC wild card playoff spot and turned back what could have been a fourth straight come-from-behind triumph for the Patriots.
Miami moved 1/2-game ahead of Baltimore for sixth and final AFC post-season spot, with the Ravens set to play Detroit Monday.
Ryan Tannehill fired three TD passes, including a go-ahead scoring strike with 1:15 left in the game. He finished with 312 passing yards on 25-of-37 efficiency as the Dolphins picked up a third straight win.
Brady racked up 364 passing yards on 34-of-55 efficiency with two touchdowns for New England (10-4).