Jones suffered the injury in training earlier this week and was sent for a scan which has confirmed he requires an extensive period of rehabilitation.
A statement issued by the club read: "Phil Jones has had surgery on a knee meniscus tear sustained in training that will require six to eight weeks' rehabilitation."
It is desperate news for the 20-year-old, who is yet to make an appearance this season.
After an extensive break following Euro 2012, Jones suffered a back injury that prevented him playing any part in pre-season.
He missed United's opening three Barclays Premier League games and the start of England's World Cup qualifying campaign, but Jones' return to training was supposed to be the prelude to his comeback.
Source: PA
Source: PA