The 26-year-old has made 208 appearances in all competitions since joining the Old Trafford giants from Blackburn in a £16.5million deal in 2011.
Jones' time at the club has been punctuated by injury setbacks, but United have seen enough to extend his stay at the club.
The England defender has signed a new and improved contract until 2023, with 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."
Jones has featured in every match since Ole Gunnar Solskjaer's arrival and the caretaker manager sees the defender as a key force within the group.
"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," the Norwegian said.
"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."