Trailing 2-1 from the first-leg following Ivica Olic's last-gasp winner in Munich, the hosts took control of the tie inside the opening 10 minutes at Old Trafford courtesy of strikes from Darron Gibson and Nani, who later added a second to give United a 4-2 aggregate advantage.
However, Olic struck again moments before half time, pulling a goal back against the run of play.
And after United's Brazilian full-back had been dismissed shortly after the interval for pulling back Franck Ribery, Louis van Gaal's side dominated and eventually grabbed the decisive goal that took them through with Arjen Robben spectacularly volleying home.
After the game both Van der Sar and Fletcher - as well as their manager Sir Alex Ferguson - accused the Bayern players of getting Rafael sent off.
"He [the referee] was pressured into giving it [the red card] by the Bayern Munich players, everyone can see that," Fletcher said.
"He decided he wasn't going to give it, then he was pressured into it."
Van der Sar added: "I think it was obvious, everybody knows who waves a card and they're very good at that.
"Initially, I thought the referee wasn't going to do it and then they put some pressure on him.
"I think it was quite obvious at 11 versus 11 that on the counter, or on the way we pressed, we would have got another."
NEWS:Robben stunner sends Bayern through
NEWS:Ferguson fumes at Rafael red card
