There was a theory that Arsenal's best chance would be to avoid them until the final, but they will instead host Atletico at The Emirates on April 26 before the second leg in Madrid a week later.
The other semi-final will be between Marseille and Salzburg, with the French side advancing following a fine comeback wins over RB Leipzig and Lazio respectively.
The midfielder was forced off on a stretcher in the first half of the match but managed to complete the game.
CSKA had grabbed a two-goal lead inside 50 minutes of the second leg, but late goals from Danny Welbeck and Aaron Ramsey eased nerves and sent Arsene Wenger's side through. "You can't say they are mentally weak, they might be physically not as big as a lot of teams but they turned it round to 2-2, so that's a big plus for them as well".
Atletico lost their second-leg last night against Sporting Lisbon but Wenger won't be under any illusions: he knows, the Spanish side will provide Arsenal's sternest test yet. The competition is now the club's priority and striker Alexandre Lacazette has said that winning it would save Arsenal's season and could mean Wenger stays on as manager for another year.
"They are a similar kind of club to us", Atletico director Clemente Villaverde said at the draw at UEFA's headquarters in Nyon.
Sitting sixth in the Premier League, only winning the final in Lyon on May 16 will take the Gunners into the Champions League next season.
Atletico are considered the clear favourites to win the competition for what would be the third time in their history, while pressure is increasing on Arsenal to lift the trophy following a turbulent domestic campaign.
The semi-final first legs will be played on Tuesday, April 24 and Wednesday, April 25. The teams also drew 0-0 at the Velodrome.