Jones, 26, joined from Blackburn Rovers in 2011 and has won one Premier League title, an FA Cup and Europa League in 208 appearances for the club.
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.
“I am excited about the challenges that lie ahead of us as we prepare for a very busy period in the season. I would like to thank Ole and the coaching staff for their continued support in my development.”
Solskjaer believes Jones is coming into his prime.
“Phil knows what it takes to be a Manchester United player. He has won the Premier League, FA Cup and Europa League and is now one of the senior players within the team,” said the interim boss.
“He is coming up to his 27th birthday and entering into his prime years as a centre-half. We are delighted Phil has committed his future to the club.”
Last week Anthony Martial signed a new contract until at least 2024 while Chris Smalling, Luke Shaw and Scott McTominay all agreed new deals earlier this season.
Negotiations are ongoing with Ander Herrera and Ashley Young, who are reportedly close to extending their current deals beyond the end of the season.