The 30-year-old has agreed a contract that will expire at the end of the current season.
"I'm really pleased to get the move completed and I'm looking forward to playing my first game," the 30-year-old told the club's official website. "I think it's a good move for myself and I'm looking forward to meeting my teammates. I've spoken already with René Meulensteen and I think it's the right club for me.
"This is a club with a great history and I always enjoyed playing at Craven Cottage, I really like it as a stadium. It's not one of the biggest but it's got something special."
Heitinga made 140 appearances for the Toffees, whom he joined from Atletico Madrid in 2009.