The England international clashed heads with Jonathan Walters before halftime, while the Northern Irishman was withdrawn early on.
|By Gary Maiden at the Britannia
The injuries are piling up for Manchester United as Phil Jones is stretchered off after a nasty clash of heads. He has been replaced by Danny Welbeck and the visitors only have one more change to make.
He was surrounded by medical staff and loaded onto a stretcher after around five minutes of treatment, before having a scan at a local hospital.
"Phil Jones looks like a concussion, he's been checked and he looks ok. The medical team dealt with it very well," David Moyes told Sky Sports after the match.
Danny Welbeck replaced his fellow England international, with Michael Carrick dropping into the defense alongside Chris Smalling.
Moyes also confirmed that Jonny Evans picked up a calf injury in the first 10 minutes.
The Northern Ireland international was replaced by Rafael early on.
Stoke was 1-0 up thanks to a deflected Charlie Adam strike by the time Jones was withdrawn.
Robin van Persie equalized after halftime but Adam struck his second to inflict a sixth defeat in eight games on Moyes' men, including the penalty shootout loss to Sunderland in the Capital One Cup.