The England star, who was the subject of a second rejected bid from Chelsea this weekend, was expected to face AIK in Stockholm on Tuesday but has been left behind due to a shoulder injury, according to United boss David Moyes.
"Wayne hurt his shoulder in a fall during a match on Saturday," 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."
Rooney's absence, just hours after United confirmed they had turned down an offer - thought to be in the region of £30m - for his services, will feed already fevered speculation about his future at Old Trafford.
Chelsea boss Jose Mourinho, who admitted last month that Rooney was his sole summer target, had seen one bid of around £20m rebuffed before an improved figure was knocked back on Sunday.
Rooney, with two years left on his current deal, is reportedly ready to try and force through a move by handing in a written transfer request but United reiterated their hardline stance on Monday morning.
"A bid was received yesterday (Sunday) and immediately rejected," a United spokesman said. "Our position remains that he is not for sale."
Nemanja Vidic will skipper the United side in Sweden after missing the first leg of the tour due to a sciatica problem, while Portuguese winger Bebe, signed for £7.4m in 2010 but yet to start a game in the Premier League, is also in the squad.