Yobo was hoping to complete his move to the Turkish side in June and the deal has now been confirmed to take the Nigerian to Turkey on a permanent basis.
"I would love to thank Everton and the management of Fenerbahce for reaching a deal," Yobo told Everton's official website.
"My family have settled well in Turkey and enjoy the life there, so I'm glad they will be re-uniting with friends here.
"It's been a long journey into achieving this dream and now is the time to pay the club and fans back with a great performance."
Yobo played for Everton for 10 years, initially joining on loan in 2002, although he spent the final two seasons on loan at new club Fenerbahce.