The Northern Ireland international, 24, has added two years to the deal that was due to expire in 2014.
He has reportedly signed improved terms of around £65,000 a week.
“I’m delighted to sign my new contract," he told the club website. "I am so proud to play for such a great club, and there’s no better feeling than playing football in this team and winning games.
“I have always felt that this is the right club for me. Even when I was 9 or 10 years old back home in Northern Ireland, clubs asked me to go on trial but I didn’t go because I knew that Manchester United was the place I wanted to play football.
"I would love to play here throughout the rest of my career.”
Boss Sir Alex Ferguson added: “Jonny has risen through the ranks to become an integral part of the first team squad. He has developed into a top player for us and has scored a couple of important goals this season too. I am delighted he has signed a new contract.”
Belfast-born Evans joined United on schoolboy terms in 2004. He has gone on to make more than 100 first-team appearances for the club, and has been capped 31 times by Northern Ireland.
This season he has been their main centre-half due to injuries to Rio Ferdinand, Nemanja Vidic, Chris Smalling and Phil Jones.
He has scored three goals in 15 matches.