The England international had to be substituted after accidently headbutting the back of Stoke forward Jon Walters' head in an aerial challenge, as United slipped to a 2-1 loss at the Britannia Stadium.
Jones' injury posed a problem for Moyes, who had already lost Jonny Evans from his defence in the game to a hamstring issue, as Wayne Rooney was forced to drop into midfield to cover the former Blackburn Rovers man's absence.
Two goals from Charlie Adam ultimately sealed Stoke's win - their first over United since 1984 - with Robin van Persie's effort continuing his good form since returning from injury, but ultimately counting for little.
Moyes was left to bemoan his side's misfortune after the match, although had good news over Jones, who is not expected to be out long-term.
"Phil is okay," said 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."
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