The Manchester United star was withdrawn in the first half against Hull City, prompting concerns about his participation in the England squad at the World Cup this summer
Jones collided heavily with Maynor Figueroa at a corner and was immediately substituted, while pitchside reports claim that the 22-year-old had his arm in a sling, plunging his World Cup hopes into doubt.
"Phil Jones has gone to hospital," confirmed Ryan Giggs after the match.
"Hopefully he will be okay; it's too near to say what his condition is.
"We'll have to see how he goes but it didn't look great."
Nemanja Vidic was brought on for the youngster, making his final appearance at Old Trafford in a United shirt ahead of his summer move to Inter.
Jones looked set to be among Roy Hodgson's defenders in Brazil this summer, having featured frequently in international squads alongside first-choice centre-backs Gary Cahill and Phil Jagielka.
He has made over 100 appearances for the Red Devils since joining them from Blackburn in June 2011.