The shock omission from the starting line-up for United's biggest game of the season in the second leg of their last 16 tie against Real Madrid was overshadowed by the controversy surrounding Nani's red card and Cristiano Ronaldo's Old Trafford return.
Before the game, manager Sir Alex Ferguson said the England forward was on the bench because he had not had enough match action after injury but afterwards, with Ferguson too upset to talk, assistant Mike Phelan said the move had been tactical.
"In that dressing room, everyone was fit," Phelan told a news conference after United went out 3-2 on aggregate after a 2-1 defeat on the night. "But big decisions have to be made."
Alarm bells might be ringing for Rooney when he considers the fate of previously key United players who have been dropped for huge games.
Take David Beckham who started on the bench for Real's 2003 trip to Old Trafford before leaving the club that summer or Ruud van Nistelrooy who was benched for the 2006 League Cup final and a series of other games before departing that year.
With striker Robin van Persie enjoying prolific form in his first United season with 19 league goals to his name and Rooney sidelined with a knee injury, the English player has not been grabbing as many headlines as he might.
He has, nevertheless, netted 11 league goals including one against Norwich City last weekend and might therefore have expected a bigger role against Real Madrid than coming on as a 73rd minute substitute when his team were behind.
"Maybe the writing is on the wall for him," former United midfielder Roy Keane said in the ITV studio before the game.
The demotion of Rooney is a far cry from his surprise inclusion in the starting line-up in the second leg of the Champions League quarter-final against Bayern Munich in 2010 when he played despite an injury.
Once branded a "genius" by Ferguson, who persuaded him to stay at the club when he wanted to quit in October 2010, Rooney has been given a message he is no longer the main man.
He had a good chance to score after coming on against Real but sent his effort over, while players who were picked ahead of him were some of United's best performers with Danny Welbeck and Ryan Giggs at the heart of their best attacking moves.
Real manager Jose Mourinho said Ferguson's judgment over his line-up should not even be being questioned.
"Sir Alex has won the right for every decision to be correct and never have a question mark against them," he told a news conference. "He is the best. He is the top.
"You are nobody, I am nobody (to question his decisions). He did a great job."
United's next team sheets will be scrutinised for further clues about Rooney, starting on Sunday when they host Chelsea for a place in the FA Cup semi-finals.
They will then turn their attention to making sure the 12-point lead they hold at the top of the Premier League translates into a 20th league title come the end of the season.
Picking themselves up from their European despair will not be a problem, according to Phelan.
"Disappointment in football is a part of the game," he said.
"For us as a football club, we've been here before and we shall bring the players together again, possibly on Thursday. We'll look at certain things and we will kick on now.
"It's very important now that we finish the season well, we're in the FA Cup still, we've got a great opportunity in the league and I'm sure that will drive the players forward in order to achieve something."