Equally, it could be argued that it represented yet another opportunity missed for the frontman to truly make his mark on a huge game on the world stage.
Often regarded as a big-game player, the England striker did not play well at all at the Allianz Arena. Two chances – gilt-edged and waiting to be buried – went begging at vital times as United crashed out in Germany.
All the pre-match hype was centered on him, both at home and abroad. Pep Guardiola, not one for hyperbole, described Rooney as one of the best players he has ever seen. The talk of a toe injury, he was certain, was smoke and mirrors. "He will play," he insisted.
Picked to support the leggy threat of Danny Welbeck, Rooney began in the deeper-lying playmaker role he has come to make his own. In the Premier League this season he has been a menace to defenders, a rare ray of light in a troubling, uneven season. He is, according to many United fans, back to his best.
At the Allianz Arena, he was limp. Moyes admitted afterwards his gamble of playing Rooney when not fully fit had "backfired". It is a recurring theme across Rooney's career. It is becoming a worrying habit.
As usual, there was little wrong with Rooney's vision, his eye for a pass, his endeavor. Finding teammates was never an issue. It was finding the back of the net where he hit a brick wall.
In big games, big players are expected to step up. Arjen Robben, on the other side, did just that, slaloming through the United defense, assisting Thomas Muller's second goal and scoring the third himself. When Bayern attacked Robben led the charge, as he so often does.
Rooney left that role to Welbeck and, on occasion, Shinji Kagawa. He was not at his brilliant best and United paid the price. Not since the days of Cristiano Ronaldo has the club been so reliant on one player and when Rooney does not play well – as is the case with Eden Hazard at Chelsea – United invariably struggles.
His ability, of course, is unquestioned. He can pass the ball 50 yards, score from anywhere on the pitch – as he so gleefully proved against West Ham earlier this season – and can control the tempo of a match.
Yet he has not joined the elite, for the sole reason that he has yet to prove unequivocally that he can produce in the big matches, time and again, when it matters most. Cristiano Ronaldo and Lionel Messi are the best players in the world for a reason: they score every week and they have the ability to drag their team to glory when they are behind.
Rooney, for now, is clinging in the second tier of football's talent list. In 2010, before a season-ending injury sustained at Bayern he was the third best player in the world. He was almost untouchable. It remains a huge pity, then, that he's never recovered or pushed on from that blistering form.
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His big performances, for both England and United, are too occasional. He has scored world-class goals in big Premier League matches – Manchester City knows that all too well – but in Europe, against the world's elite, he has not managed to do it. A goal in the 2011 Champions League final, which United lost, is the fruit of his big-match European labors. That goal against Barcelona at Wembley was identical to his second effort against Bayern on Wednesday - the difference being that in Munich the ball barely had enough power behind it to roll out of play.
Since bursting on to the international scene at Euro 2004 he has also flattered to deceive. Injuries, again, can be blamed for his abject displays at the 2006 and 2010 World Cups but he had no such excuse at Euro 2012. He just did not turn up.
This is not to say Rooney cannot. On his day he remains England's talisman and United's best player, despite the presence of Juan Mata and Robin van Persie. He has time on his side; at 28, Rooney has another five years at the top, at the very least.
With David Moyes set to embark on a summer overhaul he is likely to be the centerpiece of a team filled with even more firepower from the beginning of next season, which will only improve his goal ratio.
That new-look United will be spearheaded by a responsible Rooney, one who is likely to have the captain's armband. With his 300,000 pound-a-week salary, he is unquestionably seen as the man to lead United in the Moyes era, and is likely to break the club's all-time scoring record along the way.
Yet he needs to do more.
He needs to become a player who can drag the team, kicking and screaming, over the finish line when the going gets tough. He needs to take up Ronaldo's mantle at the club and earn his legendary status. He needs to shake the habit of entering key tournaments and matches half fit.
United needs Rooney more than ever and now is the time to truly deliver - before it's too late.