Rooney sat out Saturday's trip to Norwich, but returned to play the full 90 minutes in Wednesday's 2-1 home defeat by Tottenham.
The forward looked some way short of full fitness. However, with Robin van Persie still not ready to return from a thigh problem, Moyes does not have the option of merely offering Rooney an extended break.
"If I could (rest him), I would," said Moyes.
"He has missed a couple of games with his groin and may well miss some more in the games coming up.
"But the longer it went on (against Tottenham), we had to try and get more attacking players on the pitch to find more ways score."
Danny Welbeck did pull a goal back after Emmanuel Adebayor and Christian Eriksen had struck for the visitors, but it was not enough to stave off a fourth home defeat of the campaign, the quickest United have reached that unhappy position since 1986.
With Tottenham leapfrogging them, United are now seventh in the table, five points adrift of the final Champions League place and 11 behind leaders Arsenal.
Yet Moyes insists his plans for the transfer window, a notoriously difficult time to bring in players of quality, remain unaffected.
"The result today would never have any effect on what we do, whether in January or the summer," he said.
"It wasn't our day but it won't change the way we go about our business."
If, after a run of six successive wins, it was a case of two steps forward and one back for United, Tim Sherwood's honeymoon period at White Hart Lane continues.
Spurs have collected 10 points from a possible 12 over the festive period, providing the perfect platform to head into Saturday's FA Cup showdown with Arsenal.
And Adebayor is a man transformed, scoring four goals in five games since being brought in from the cold by Sherwood after his exile under Andre Villas-Boas.
"We know he is one of best in league and when he performs as he is at the moment he's almost unstoppable," said Sherwood.
"I have no reason to believe he won't keep it going.
"He's massively important to us. He seems happy in himself and wants to play every minute.
"I am amazed (how quickly he has reintegrated) because he's not had too much of a pre-season either."
As Sherwood noted, it makes Adebayor susceptible to injury and the Togo forward was carried off immediately after Welbeck's goal, apparently with an acute case of cramp.
"It's always a danger you're going to break down and I hope he's not too badly injured," said Sherwood.
"He's got ice on every part of his body so we're not sure which (part) is hurting him more."