The striker missed the club's entire tour of the Far East and Australia with a hamstring complaint, but following his appearance in a behind-closed-doors encounter against Real Betis at the weekend, he had been expected to feature against AIK in Stockholm.
However, manager David Moyes has revealed that the 27-year-old damaged his shoulder during Saturday's match.
"Wayne hurt his shoulder in a fall during a match on Saturday. It's not too serious and I don't expect it to keep him out for too long," Moyes told the club's official website.
"I'm disappointed he's missing the game because we were keen to get him back involved and ready to play."
News of Rooney's absence is likely to lead to more speculation regarding his future at United, who rejected a second bid for his services from Chelsea earlier today.