The Spanish outfit will host the Bundesliga champions at the Bernabeu for the first leg, with the deciding fixture being held at the Allianz Arena towards the end of the month.
Bayern were able to see off Manchester United 4-2 on aggregate to keep their hopes of clinching consecutive titles alive.
The two giants have met in the European Cup 20 times in their history, including five semi-finals, four of which ended in Bayern's favour.
Meanwhile, Chelsea will go up against Atletico Madrid in the final four.
All semi-final ties will be played across April 22/23 and April 29/30.