Rooney was lying injured in his own half as Bayern broke forward on their fateful attack.
Ivica Olic applied the cool finish for Bayern's winner after robbing Patrice Evra of possession in the box, and at that moment United medical staff instantly ran to Rooney, who appeared to land awkwardly on his right ankle after trying to avoid having his left foot trodden on by Mario Gomez.
Rooney had earlier scored his 34th goal of the season before deflecting Franck Ribery's free-kick past Edwin van der Sar 13 minutes from time.
The initial fear was that it was another of those dreaded metatarsal injuries and while that did not seem to be the problem on closer inspection, any enforced lay-off at this stage of the season will be bad news in particular for Manchester United boss Sir Alex Ferguson.
The night could scarcely have started better for the England striker.
Even by Rooney's remarkable standards, meeting his boss' demand for an away goal after just 64 seconds was a staggering achievement.
Much of the period that did elapse was for treatment to Nani, who had been so needlessly chopped down near the corner flag by Bayern's man-in-the-mask Martin Demichelis.
It turned out to be the start of a complete disaster for the Argentina defender, who slipped as he attempted to reach the ball when Nani eventually took the free-kick and it looped skywards off Mark van Bommel.
All on his own, four yards out, Rooney had the simplest of tasks to tap home and leave the hosts, already without Arjen Robben, in a state of complete shock.
By the time they revived themselves, the hosts could have been out of the contest completely as Paul Scholes, surprisingly preferred to Antonio Valencia, put the ball over.
United knew the fightback would come though. German teams are not noted for giving up on their own patch, especially not a club with a tradition as proud as Bayern's.
It was probably just as well for the Red Devils that Robben was missing for with a bit of additional guile, Bayern would surely have been on terms at the break.
The first came through a moment of brilliance from the mercurial Franck Ribery, who chipped beyond the United defence, straight to Hamit Altintop.
A first-time finish was demanded. Unfathomably, with only Edwin van der Sar to beat, the Turkey star tried to control and succeeded only in rolling the ball through to the veteran Dutchman.
Ribery was the architect of Bayern's second opening too as Van der Sar punched away his angled drive.
Altintop failed to make a decent connection with his shot, but the direction caught Rio Ferdinand out as it rolled through to Ivica Olic.
To his team-mates' disbelief, Olic failed to make any contact and the ball trundled wide.
Although he had not given that impression before half-time, Altintop can clearly play, judging by the twinkle-toed way he danced through the United defence in a one-sided start to the second period.
Van der Sar was intent on not being beaten though.
He may have another year's contract that will keep him at Old Trafford beyond his 40th birthday, but the veteran Dutchman knows opportunities to appear on the greatest stage are reducing and his save to deny Altintop suggested he wants to reach a third final in a row in Madrid on May 22.
There was nothing Van der Sar could do to prevent Bayern's equaliser 14 minutes from time though.
Gary Neville will have plenty of time to reflect on the handball near the edge of his area that cost him a booking and offered Ribery the chance to shoot.
After causing so much damage to opposition defences this season, maybe it was a collective defenders' retribution that ensured Rooney was the man who Ribery struck to send the ball flying into the corner.
It was the least Bayern deserved.
But worse, possibly much worse, was to follow after Nemanja Vidic had thundered his header against the crossbar.
Gomez tried to burst forward after his collision with Rooney, and although Vidic's challenge steered the ball towards Evra, the Frenchman was caught unawares by Croatia striker Olic who steadied himself before steering the ball past Van der Sar.