The centre-back was visibly struggling to get around the Wembley pitch from the first moments of Friday's friendly, and almost allowed Leroy Sane to open the scoring.
And with just 24 minutes played Jones went down, and was unable to play any further part in the encounter.
Jones' left groin was heavily strapped by the England medical team, but there was no need for a stretcher as he limped slowly off the turf.
Liverpool's Joe Gomez was the man chosen to replace the defender, making his international debut for the Three Lions in the process.
United will be now crossing their fingers and hoping Jones' groin trouble is minor, as manager Jose Mourinho faces the prospect of another name on his injury list.
Paul Pogba, Marouane Fellaini, Michael Carrick, Zlatan Ibrahimovic and Marcos Rojo have also been ruled out for the Special One, who said last week he would not moan about injury troubles.
"I think it's my fault because I should cry every week about our injuries and remind everybody day after day or press conference after press conference," he pointed out.
"It's my decision, it's my way of dealing with problems, it's my way of trying to motivate and give confidence to the players that are going to replace people but again maybe I have to reconsider my profile.
"I know that I moan with a lot of things but I don't do with injuries and probably I should."