The England defender has suffered injury problems and dips in form in his time at Old Trafford but played in all 10 of Ole Gunnar Solskjaer's unbeaten matches since the Norwegian took caretaker charge.
The contract includes the option to extend by a further year. "I am delighted to have signed a new contract," Jones said. "Manchester United has been a big part of my life for eight years and I love everything about this club.