Everton and Fenerbachce signed the deal on Friday night and the Nigerian defender signed his new terms on Saturday morning.
The 31-year-old signed a three-year contract with the Turkish heavyweights where he has been on loan for the past two seasons.
The deal looked all but done last week, but talks broke down over additional demands by the English club, including a 1.5million Euro apparance related bonus payment.
The Nigerian captain was initially loaned to Fener after falling out of favour with David Moyes and the initial arrangement was for a permanent move for 4-million Euro.
Yobo joined Everton from Marseille in 2002 and made more than 250 appearances for The Toffees.