The 31-year-old Nigerian, who has spent the last two seasons on loan at the Turkish club, has singed a three-year deal.
Yobo told the Toffees' official website, www.evertonfc.com: "I would love to thank Everton and the management of Fenerbahce for reaching a deal."
He added: "My family have settled well in Turkey and enjoy the life there, so I'm glad they will be re-uniting with friends here.
"The permanent switch is done and I am also switching to help the team do well on the pitch.
"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."
Nigeria international Yobo joined Everton from French club Marseille, initially on loan, in July 2002 as manager David Moyes' first signing, making a permanent £3.5million switch the following summer.
He made more than 250 appearances for the club, the last of them in a 0-0 Barclays Premier League draw at Stoke in May 2010.
His contract at Goodison Park was due to run until the summer of 2014.
Source: PA
Source: PA