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's Twitter account.
A post on the club's official feed read: "@WayneRooney misses out on the final #mutour match due to a shoulder injury sustained at the weekend. David Moyes: "It's not too serious."
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 only fuel speculation about his future at Old Trafford.
Chelsea boss Jose Mourinho, who admitted last month that Rooney was his sole summer target, had already seen one bid of around £20m rebuffed before an improved figure was knocked back on Sunday.
Rooney, who has 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.
"A bid was received yesterday (Sunday) and immediately rejected," a United spokesman said. "Our position remains that he is not for sale."