Jones, 26, has made 208 appearances for the Old Trafford club – including 16 this season – since arriving from Blackburn Rovers for £17m in 2011.
United interim manager Ole Gunnar Solskjaer said the new deal for the England centre-back is a sign the club are planning ahead.
“I have a vision of what this club will look like in two years,” he said.
United have won nine games out of 10 since Solskjaer took over as caretaker manager on 19 December, following the dismissal of Jose Mourinho.
The Norwegian has been told he will be in charge for the rest of this campaign and no decision has yet been taken about whether he will get the job on a permanent basis.
Jones, whose contract was due to expire in the summer, has signed his deal a week after Belgium midfielder Marouane Fellaini left United to take up a lucrative contract in China.
“Phil has won the Premier League, FA Cup and Europa League and is now one of the senior players,” said Solskjaer.
“He is coming up to his 27th birthday and entering into his prime years as a centre-half.”
United, who travel to Fulham on Saturday (12:30 GMT kick-off), are challenging for a top-four place in the Premier League.
They also play Paris St-Germain in the first leg of their Champions League last-16 tie and face Chelsea in FA Cup fifth round during February.
“I am excited about the challenges that lie ahead of us as we prepare for a very busy period in the season,” said Jones.
“I would like to thank Ole and the coaching staff for their continued support in my development.”