Thomas followed Chris Chambers, who won the offensive award for his game against Buffalo, and Jason Taylor, who was honored for his play in the Oakland game.
Against San Diego, Thomas had a team-high 11 tackles and an interception in his first game back after missing two games because of ankle and shoulder injuries.
Thanks to Thomas' efforts, the Dolphins were able to hold All-Pro Bowl running back LaDainian Tomlinson to 75 yards rushing.
"I felt good," Thomas said after the game. "I wasn’t moving as well as I’d like to, but I watched a lot of tape on San Diego. I’m glad to be back. It drives me crazy to be out. We just kept grinding out there. We played hard, but we can play better. We’re getting better as we keep going. I’m proud of the guys who stepped up today."
This marks the third time in Thomas' 10-year career that he has been named AFC Defensive Player of the Week and the first time since 2001. He is the third Dolphins defensive player to win the award this season, following Taylor and safety Lance Schulters, honored for his play in the Carolina game.