The Premier League champions had earlier advertised on their Twitter account that the striker would make his return from a hamstring injury in Tuesday's match.
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"Wayne hurt his shoulder in a fall during a match on Saturday," manager David Moyes told the club's official website. "It's not too serious and I don't expect it to keep him out for too long.
"I'm disappointed he's missing the game because we were keen to get him back involved and ready to play."
Goal has previously revealed that the striker fears a backlash from fans if he is to represent the club again, and feels there is no way back from him at Old Trafford.Former United boss Sir Alex Ferguson claimed at the end of last season that Rooney asked to leave the club for a second time, and fans subsequently booed the striker when he collected his Premier League winner's medal and boarded the team bus for their trophy parade.