Rooney has been nursing a groin problem and sat out the trip to Norwich on December 28.
The 28-year-old did return for the New Year's Day home defeat by Tottenham, but was pictured on Friday leaving a private hospital in Manchester having had further scans to establish the extent of the injury.
United have given no update on Rooney's fitness.
However, with a trip to Sunderland for the Capital One Cup semi-final first-leg looming just 48 hours after the Swansea encounter, Moyes has already decided Rooney will not face Michael Laudrup's men.
"He's got a groin injury and won't be available on Sunday," Moyes told reporters.
"He's got a chance [of facing Sunderland]."
Rooney's absence will be keenly felt given his contribution this season.
And an apparent preference not to enter into negotiations over a contract extension until after the World Cup must be some kind of concern given United's present seventh place in the table.
"We would have to wait and see what [would] happen if that situation arose," said Moyes, when asked whether the chances of Rooney staying would be adversely affected by United failing to secure a place in next season's Champions League.
"But if you looked at his performances you'd have to say he's certainly playing at his best."
Moyes has also ruled Robin van Persie out of the Swansea game as the Dutchman is still to recover from a thigh problem that has kept him out for six games.
With Ashley Young facing a spell on the sidelines after sustaining a shoulder injury in his attempt to avoid Hugo Lloris' wild lunge, Nani no nearer recovering from a hamstring injury that has already kept him out for a fortnight and Marouane Fellaini recovering from wrist surgery, Moyes' squad is being stretched.
The United manager insists his depleted resources will not force him into the transfer market against his better judgment, underlining his belief January is not the greatest time to do business.
"It won't change how we go about things," said Moyes.
"January is not an easy month to purchase in.
"We have a good, big squad that is getting stretched at the moment because of the number of games.
"But everybody picks up injuries at this time of year. We are no different and we will use the players."
However, Moyes has revealed he will not be put off buying players just because they are ineligible to figure in the Champions League.
"It's not the biggest thing because obviously you've got other games to play - FA Cup ties, League Cup ties hopefully, Premier League games," said Moyes.
"But I do think you'd like them to be ready to play in the Champions League as well."
However, Moyes has no intention in getting involved in discussions over individuals, and that includes Juan Mata, with whom United were linked in the summer.
That interest may be resurrected amid suggestions the Spain midfielder is unhappy with life at Chelsea, where he has failed to win over Jose Mourinho.
"I never talk about players at other clubs," said Moyes.
"That's my stock answer. I don't think it is right.
"I didn't do it in the summer and I certainly won't do now."
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