The England international, who is expected to be named in Roy Hodgon's squad to face Scotland next week, picked up a shoulder injury on Saturday against Real Betis which caused him to miss their friendly in Sweden against AIK Stockholm earlier this week.
Moyes confirmed in a press conference that Rooney probably won't make the trip to Wembley with the side on Sunday.
"I don't think he is going to be fit and available. Of course we are still hoping he will, but I have a feeling he won't make it," said Moyes.
Rooney has been strongly linked with a move to Arsenal and Chelsea this summer.