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.
In addition, he will miss at least the Red Devils' opening three Champions League group matches.
Even when he has recovered, Jones' lack of match fitness may prove a significant problem in regaining the form which at one stage saw him compared to Duncan Edwards during an exceptionally encouraging debut campaign following his big-money move from Blackburn in 2011.