Jones was taken to hospital following the first-half incident with with Jonathan Walters, although he was able to return to the ground and link up with the rest of his team-mates after United's 2-1 defeat.
"Phil is okay," said United manager David Moyes. "He has been checked at the hospital.
"He was out for a little while. I saw him falling back and his head going back on the grass. He got up but when we went to treat him he lost consciousness for a while.
"The medical team did all the right things. They got him to hospital but he is fine. It looks like concussion. He should be okay."
Jones' exit followed that of central defensive partner Jonny Evans, who suffered a calf injury as the bad luck that has dogged Moyes throughout his short time at Old Trafford surfaced again.
Even the details of a first ever Premier League defeat to Stoke, and a first loss at the Britannia Stadium, showed how ill fortune has attached itself to the Scot given Charlie Adam's opener came courtesy of a massive deflection off Michael Carrick.
Robin van Persie equalised early in the second half, only for Adam to seal victory with an exquisite 20-yard strike.
"I thought we were the better team," said Moyes.
"We got to the byline eight, nine, 10 times but the ball back never picked someone out in the box. That was our undoing.
"In the end we lose to a free-kick from 30 yards with a massive deflection and a worldy (a world-class strike)."
The result deals a massive blow to United's chances of qualifying for next season's Champions League.
If Liverpool beat West Brom on Sunday, Moyes' team will be nine points adrift of fourth spot and seemingly incapable of stringing the results together required to force their way up the table.
They have now lost eight times this season.
And after West Brom, Everton and Newcastle all broke long sequences without winning at Old Trafford, Stoke have now done it on home soil against United.
The last time they defeated United in a league game was on Boxing Day 1984, so long ago the match was played at the Victoria Ground and current Stoke boss Mark Hughes was a 20-year-old striker for the Red Devils.
"I can't remember that one," said Welshman Hughes.
"The one I do remember was in the League Cup (in 1993). I lost at the Victoria Ground, which tells you how long ago that was.
"I was at fault for one of the goals."
The latest success was more remarkable for the fact Stoke had fallen into the bottom three at kick-off, only to take a massive leap out.
"At the start of proceedings we were in the relegation zone," said Hughes.
"We have ended up 11th. That tells you how crazy the league is at the moment."