Bayern will face Zenit St Petersburg in the semi-finals after the Russian champions eased through 4-2 on aggregate against Bayer Leverkusen, despite losing their home leg 1-0 on Thursday.
In the other semi-final Fiorentina, losing finalists in 1990, will meet Scottish league-leaders Rangers after both clubs also eased through their respective quarter-final ties against PSV Eindhoven and Sporting Lisbon.
In Spain, Cosmin Contra opened the scoring for Getafe just before halftime, but Bayern's French winger Franck Ribery scored an equaliser in the 89th minute to stun the home crowd.
|"I have to compliment Getafe and Laudrup as they played a great game and were on the point of humiliating us."|
Bayern Munich manager
Further excitement followed when Getafe took a 3-1 lead in the first three minutes of extra time with strikes from Francisco Casquero and Braulio, but then heartbreak for Getafe as Toni struck a late double.
Roberto Abbondanzieri, Getafe keeper, dropped a Mark van Bommel cross at the feet of Toni who fired in from close range in the 115th minute, before the Italy striker headed home in the final minute of extra time to earn his side a remarkable comeback win.
Michael Laudrup, Getafe coach, said his team were bitterly disappointed at the harsh manner of their exit.
"It is difficult to pick ourselves up after this but life goes on and after a couple of days the team will realise that they did something incredible out there," said the Dane.
Ottmar Hitzfeld, Bayern coach, praised the opposing players and coach having previously said before the tie that he knew nothing about them.
"I have to compliment Getafe and Laudrup as they played a great game and were on the point of humiliating us. They were the best team tonight," Hitzfeld admitted.
Meanwhile in Eindhoven, Romania striker Adrian Mutu sent Fiorentina into the final four after his double strike sealed a 2-0 away win over PSV for a 3-1 aggregate victory.
Mutu gave the visitors a deserved lead late in the first half, and sealed the tie with a fine curling finish on 53 minutes.
"The important thing is to have gone through but then I am very happy with my goals, especially the first which was really great," Mutu told La7 television.
|"We are proud of being the last Italian side in Europe and now we will try and go to the end."|
"We are proud of being the last Italian side in Europe and now we will try and go to the end."
Rangers, who have already won the Scottish League Cup this season and are in pole position to reclaim the league title from arch rivals Celtic, scored two second-half goals against Sporting through Jean-Claude Darchville and Steven Whittaker, taking a 2-0 win on aggregate.
Finally Zenit, the only team left in the competition never to have won a major European trophy, could not replicate their 4-1 destruction of Leverkusen in Germany last week, but did enough at the Petrovsky stadium to reach the last four for the first time.
Dmitri Bulykin, Leverkusen's Russia striker, gave the German club some hope with an 18th-minute header but Zenit held on for a 4-2 win on aggregate.