The Dutch defender's arrival was confirmed by the west London outfit soon after the Cottagers announced Philippe Senderos' move to Valencia
The news of the Dutch defender's arrival at Craven Cottage came shortly after the announcement that fellow centre-half Philippe Senderos had departed for Valencia for an undisclosed fee.
Heitinga has signed a deal until the end of the season, having fallen out of favour at Goodison Park.
He told Fulham's official website: "I'm really pleased to get the move completed and I'm looking forward to playing my first game.
"I think it's a good move for myself and I'm looking forward to meeting my team-mates. I've spoken already with (head coach) Rene Meulensteen and I think it's the right club for me.
"I chose Fulham because the feeling was good and what was also important was the conversation between me and Rene.
"He knows exactly what he wants and I know exactly what I want. The main thing is to keep Fulham in the league and hopefully the boys will start with a win against Southampton."
Everton boss Roberto Martinez added: "Johnny has left with our best wishes and we hope everything goes as planned and he can get in the [Netherlands] World Cup squad.
"He has been a terrific servant and we wish him well."
Heitinga joins Fulham with the club 19th in the Premier League, having played 140 times for Everton following a move from Atletico Madrid in 2009.