French club Marseille will play Red Bull Salzburg in the other semifinal.
Arsène Wenger’s Arsenal will play the first leg at the Emirates Stadium against Atlético, led by French striker Antoine Griezmann, who are favourites to win the competition for the third time.
The first legs will take place on April 26 with the second on May 3.
Arsenal reached the last four after surviving a scare against CSKA Moscow in Thursday’s quarterfinal second leg in the Russian capital.
Danny Welbeck and Aaron Ramsey both scored late in the game for Arsenal to calm nerves after CSKA had raced into a 2-0 lead on the night. The London side won 6-3 on aggregate.
Atlético lost 1-0 to Sporting in Lisbon on Thursday but advanced 2-1 on aggregate.
Marseille overcame a first-leg deficit to beat German side Leipzig 5-3 over two legs in their quarter-final, while 1994 finalists Salzburg produced the shock result of the night by defeating Italian side Lazio 4-1 at home to win 6-5 on aggregate.
Salzburg have already beaten Marseille once in the competition this season, a 1-0 victory in Austria. The teams also drew 0-0 at the Stade Velodrome.
“But this time it’s the semifinal so it’ll be different,” Marseille director Andoni Zubizarreta told beIN Sports.