In their quest to reach a first Champions League final since 2013, Bayern will have to overcome reigning champions Real Madrid, who knocked them out in 2014 and 2017. In the other semifinal, Liverpool will face Roma.
Having wrapped up a sixth consecutive Bundesliga title, Bayern Munich are now free to concentrate on the greatest prize of all: the Champions League, which has eluded them since 2013.
After disposing of Sevilla in rather less-than-spectacular fashion, reigning European champions Real Madrid now stand between the Bavarians and this season's final in Kiev, Ukraine.
Madrid dramatically overcame Italian giants Juventus in their semifinal, a late Cristiano Ronaldo penalty sending them through after Juventus had levelled the tie at 3-3 on aggregate.
Bayern don't have the best of memories against the Spanish giants. They were beaten 6-3 on aggregate by Zinedine Zidane's side in last season's quarterfinal and were hammered 5-0 on aggregate in the 2014 semifinal.
But coach Jupp Heynckes is focussing on the positives, namely that the first leg will take place at home in Munich.
"We'll take it as it comes," he told a press conference ahead of his team's Bundesliga fixture against Borussia Mönchengladbach this weekend. "I have good memories of [knock-out ties] from our treble-winning season [in 2013]. We played at home first against Barcelona and against Juventus."
"In 2012, we played at home first against Real Madrid in our semifinal and went through. So I'm confident. I don't consider the draw particularly unlucky."
Ronaldo was on the scoresheet in both legs as Real beat Bayern in last season's quarterfinal and Heynckes was full of praise for the superstar striker.
"Cristiano is one of the most outstanding players in the history of the game," he said. "I speak regularly with Toni Kroos who tells me that Cristiano trains incredibly hard to be able to be the very best."
"But in such big games, I think the overall team performance is an important factor."
In the other semifinal, five-time winners Liverpool will face AS Roma.
Champions League semifinals:
Bayern Munich vs. Real Madrid
Liverpool vs. AS Roma
The final will take place in Kiev, Ukraine, on May 26.
Earlier in Nyon, the draw for the semifinal of the Europa League also took place – without German participation, after RB Leipzig were knocked out by French giants Olympique Marseille.
Marseille will now face Leipzig's Red Bull sister franchise from Salzburg. Under German coach Marco Rose, Salzburg knocked out Borussia Dortmund before staging a dramatic quarterfinal comeback against Lazio.
In the other semifinal, Premier League side Arsenal were rewarded for their quarterfinal win over CSKA Moscow with a semifinal tie against Atletico Madrid. The Spanish side overcame Sporting Lisbon in their quarterfinal and are the only previous Europa League winners left in this year's competition.
Europa league semifinals:
Olympique Marseille vs. Red Bull Salzburg
Arsenal vs. Atletico Madrid
The final will take place in Lyon, France, on May 16.