The 20-year-old suffered the injury during training earlier this week and was sent for a scan which has confirmed he faces a long lay-off.
A club spokesperson told United's official website, ManUtd.com: "Phil Jones has had surgery on a knee meniscus tear sustained in training that will require six to eight weeks of rehabilitation."
It is yet more bad news for Jones, yet to make an appearance this season.
After an lengthy break following Euro 2012, Jones suffered a back injury that prevented him playing any part in pre-season.
He missed United's opening three Premier League games and the start of England's World Cup qualifying campaign, but Jones' return to training was supposed to be the start of his return to full fitness.
Instead, Jones is sidelined until November.
It means he will miss England's next two qualifiers against San Marino and Poland next month.
And for United he is set to be sidelined from key league fixtures with Liverpool, Chelsea and Arsenal.
He is also set to miss the Red Devils' opening three Champions League group matches at least.
And there is no guarantee that when he does return Jones will hit the heights that saw him widely lauded during his debut season for United following a transfer from Blackburn Rovers in 2011.
Fellow defender Chris Smalling remains sidelined after breaking a metatarsal, but Jonny Evans and Rio Ferdinand have bolstered United's defence by their recent returns from injury problems.