The 18-year-old completed a medical on Thursday and has signed a five-and-half year contract with David Moyes' side.
|13/10||Everton are 13/10 with William Hill to be the only team to score when they play Aston Villa
"I am very excited to be joining Everton," Stones told the club's official website.
"I've been very impressed with everything I have seen at Finch Farm already. Now the hard work begins."
Wigan were also understood to be interested in signing the defender on Thursday, but the move broke down with the Toffees interested.
David Moyes and the Goodison Park club complete the signing after a move for Twente midfielder Leroy Fer collapsed on Wednesday, despite a fee of around £8.5 million being agreed with the Dutch outfit.