The Armenia international suffered a knee injury during the weekend defeat at Manchester United, having scored Arsenal's only goal in a 2-1 reverse.
And while he has been passed fit to play, he will begin the match as a substitute as Arsene Wenger decided not to risk the former United star in the semi-final second leg.
"It's not the best moment to explain the why of the decisions," Wenger said before the match.
"We win a game like that with 18. Everybody has the same focus. "We need strikers tonight. Everybody will have a part to play, all the big players."
Alex Iwobi was Arsenal's other fitness doubt, and also starts the clash on the bench for the visitors at the Wanda Metropolitano.
But David Ospina retains his place in goal ahead of Petr Cech despite also picking up a knock at Old Trafford.
Atletico, meanwhile, start Diego Costa and Antoine Griezmann up front in a 4-4-2 line-up as the Spanish side look to defend the 1-1 draw picked up in the Emirates Stadium.
Coach Diego Simeone is forced to shuffle his side following Sime Vrsaljko's early red card in the first leg.
Thomas Partey is moved back to the right side of defence to accommodate the defender's absence, with Kevin Gameiro dropping to the bench.
Atletico Madrid: Oblak; Thomas, Godin, Gimenez, Lucas; Gabi, Saul, Koke, Vitolo; Griezmann, Costa.
Substitutes: Werner, Luis, Torres, Correa, Savic, Gameiro, Olabe.
Arsenal: Ospina; Bellerin, Mustafi, Koscielny, Monreal; Xhaka, Ramsey; Wilshere, Ozil, Welbeck; Lacazette.
Substitutes: Cech, Iwobi, Maitland-Niles, Chambers, Kolasinac, Nketlah, Mkhitaryan.