Arsene Wenger has prioritised the competition in recent weeks with hopes of qualifying for next seasons Champions League now resting on victory in Europes second tier competition.
Arsenal have already beaten Ostersunds, AC Milan and CSKA Moscow in the knockout stages, but overcame a major scare in Russia on Thursday night.
Trailing 4-1 from the first leg, goals from Fedor Chalov and Kirill Nababkin threatened an upset before Danny Welbeck and Aaron Ramsey calmed Arsenals nerves with late strikes.
Atletico, who won the competition in 2010 and 2011 as well as reaching the Champions League final in 2014, represent the sternest possible test for Wengers side.
After last nights 2-2 draw in Moscow, the Arsenal manager said: Ideally [we would wish to avoid them].
Maybe they are the strongest on paper. Lets just play well against the team we get.
The first leg takes place at Emirates Stadium on April 26 and the return at Atleticos Wanda Metropolitano stadium a week later, with Arsenal facing a Premier League match against Manchester United at Old Trafford in between.
In the other semi final, Marseille will take on FC Salzburg who came from behind to defeat Lazio in their quarter final.
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