The draw took place on Friday morning in Nyon, Switzerland and also pitted Real Madrid against Manchester City.
Bayern will have the advantage of having the second leg at the Allianz Arena, after they make the trip to Madrid a week previous.
Battle against Benfica
It was no easy ride for the Bavarians in the last eight as they edged past SL Benfica 3-2 on aggregate.
They took a 1-0 lead to Lisbon this week, but found themselves behind after Manuel Neuer's mistake allowed Raul Jimenez to open the scoring.
Arturo Vidal and Thomas Müller scored either side of the break to put the visitors in a comfortable position; Anderson Talisca's free-kick proved to be a mere consolation.
They are now the only German side left in Europe after Borussia Dortmund and VfL Wolfsburg lost to Liverpool and Real Madrid, respectively.
Atlético will be no pushovers
After falling to their city neighbours in the final two years ago, Atléti are out to set up a possible meeting against Real and avenge that defeat.
Their incredible defensive effort, team-work and Antoine Griezmann's finishing helped them to a 3-2 aggregate win over FC Barcelona.
The most memorable meeting between the two teams dates back to 1974, and the European Cup final that year.
It looked like Luis Aragones' goal would be enough to secure the victory for the Spanish side, but Hans-Georg Schwarzenbeck's last-minute equaliser brought Bayern level.
The replay took place two days later, and Uli Hoeneß and Gerd Müller both notched up braces to seal the first of three successive European Cup triumphs.
The semi-final draw in full
First legs (26/27 April): Manchester City v Real Madrid - Atlético Madrid v Bayern Munich
Second legs (3/4 May): Bayern Munich v Atlético Madrid - Real Madrid v Manchester City