Wayne Rooney seemed to have inspired United to a famous victory as the England striker started the game after much speculation over his injured ankle.
But a late first half goal from Munich and Rafael’s sending off early in the second half proved decisive.
For forty minutes it looked like the Reds were heading for their fourth consecutive Champions League semi-final as they raced into a three goal lead.
Darron Gibson gave United the perfect start after just two minutes, colleting a Rooney pass to fire past a flat footed Hans-Jorg Butt.
The hosts were playing with so much commitment and pressure that Bayern were constantly on the back foot.
The second goal duly arrived on six minutes when Nani cheekily back-heeled Antonio Valencia’s cross.
And still United dominated and deservedly made it three just before the break as Nani again finished clinically.
This hope was turned to reality within four minutes of the restart when Rafael saw a second yellow and was dismissed by the Italian referee.
But now Bayern were building up a head of steam and subjecting United to the same type of pressurised play they had to endure in the first half.
The visitor’s only needed to score and progress on away goals.
Yet even with ten men United had chances to seal the game as Nani, Gibson and Darren Fletcher all went close.
Rooney was substituted after the dismissal and gradually the German’s made their numerical advantage count.
With seventeen minutes remaining the crucial away goal duly arrived and what a tremendous effort it was – Arjen Robben was left unmarked on the edge of the penalty area to volley an unstoppable shot past van der Sar direct from a corner.
United made substitutions but Bayern easily played out time to ensure for the first time in seven years there is no English representative in the Champions League semi-final’s.
For Bayern Munich the 4-4 aggregate result means it will be their first appearance in a semi-final since 2001.
United boss Sir Alex Ferguson felt his team had been the better outfit over the two legs and was disappointed with the behaviour of the Bayern players in surrounding the referee for the dismissal of Rafael.
“They would never have gotten through had we played with eleven men. With eleven men it was no problem.
“The young boy was inexperienced but they got him sent off. Everyone sprinting towards the referee. Typical Germans. You can’t dispute that,” fumed Ferguson to ITV1.
The key issues were the goal before half time and then the young boy getting sent off.
Ferguson refused to use fatigue as an excuse, even with ten men.
“The problem was with the extra man, they made the ball work but I still thought we defended very well and it took an exceptional goal to finish the tie.
“Overall I thought we played better than they did on their own ground.”