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Kicker Dan Carpenter ensured that the Bills were ahead at half time though, kicking three field goals against his former team before the break.
A long drive at the start of the third quarter put the Dolphins on the board, with Caleb Sturgis kicking a 34-yard field goal.
The home side increased their advantage straight from the kickoff, with CJ Spiller running the ball back 102 yards for the opening touchdown of the game.
The team exchanged touchdowns late in the third quarter, with Mike Wallace hauling in a seven-yard pass to cut the Buffalo's lead, before Watkins quickly restored the advantage with his first NFL touchdown.
Carpenter piled more misery on his old team in the fourth quarter, kicking two more field goals, while a third effort struck the post, keeping the Bills unbeaten so far this season.