United missed out on a fourth-straight semi-final spot after winning 3-2 at Old Trafford to lose the tie on goal difference, thanks to a 2-1 defeat in Munich.
Arjen Robben scored the all-important goal on 73 minutes after youngster Rafael had been sent off for a second bookable offence due to a foul on Franck Ribery.
However, Ferguson refused to point finger on the Brazilian full-back as he believes Bayern players influenced the referee's decision.
"It was 35 yards from goal (the Ribery foul), There was no threat and the referee wasn't going to do anything about it until they surrounded him," said the United boss.
"It is typical of Germans. They are like that."
"It is hard to digest something like that. It was a top performance.
"In one way you could say we have thrown it away, in another you could argue we were very unlucky."
Meanwhile, Ferguson allayed fears over the fitness of Wayne Rooney, who aggravated an ankle injury during the game, but confirmed he will be out of action this weekend.
Rafael's red card
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