The Northern Irish defender, who has made 141 appearances in his Red Devils' career so far, put pen to paper on Friday.
The 24-year-old insisted that he has always felt at home at Old Trafford, while expressing his desire to stay with the club for the foreseeable future.
“I’m delighted to sign my new contract," he told the club's official 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.
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“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 have come through the Academy here and developed as a player with the help of all my team-mates, the manager and the coaching staff. I would love to play here throughout the rest of my career.”
The centre-back joined the club's youth system as a nine-year-old in 2004, and, after making his debut against Coventry in 2007, has taken advantage of injuries to both Rio Ferdinand and Nemanja Vidic to establish himself in the first team.
Ferguson highlighted the importance of the defender to his squad, while mirroring the player's delight at the extenuation.
“Jonny has risen through the ranks to become an integral part of the first team squad," the Scot added.
"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.”