The Nigeria captain has enjoyed a successful two-year period in Istanbul, helping Aykut Kocaman's men to the Super Lig title in 2010-11 and the Turkish Cup in 2011-12.
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Yobo had been left frustrated as negotiations between the two clubs reached an impasse, but a permanent transfer, confirmed by the Kadikoy outfit, was announced on Sunday.
The 31-year-old was delighted to have sealed a move to the Sukru Saracoglu, and is looking forward to making an impact.
“I am the happiest man in the world now,” Yobo told Goal.com.
“I want to thank all my fans, friends and family who have stayed behind me, and I promise to raise the flag higher every day.”
Yobo signed a three-year contract with the Turkish giant that will see him pick up a 2 million euro annual salary. Fenerbahce will pay 2.5 million euros to Everton for his services.
Prior to his 10-year stint with the Toffees, Yobo played for Standard Liege, Olympique de Marseille and Tenerife.