The former Chelsea striker only made the bench for the first leg in London, which finished 1-1, due to the after-effects of a hamstring injury.
Atleti manager Diego Simeone has made three changes to the side which started at the Emirates Stadium, with Vitolo and Gabi joining Costa in the first XI, while Sime Vrsaljko, Angel Correa and Kevin Gameiro drop out.
Mesut Ozil and Jack Wilshere will take on key midfield roles, while Henrikh Mkhitaryan, who was withdrawn during last weekend's defeat to Manchester United with a knee problem, has been named on the bench.
Atletico Madrid: Oblak; Thomas, Gimenez, Godin, Lucas; Vitolo, Saul, Gabi, Koke; Costa, Griezmann
Subs: Luis, Torres, Correa, Savic, Gameiro, Werner, Olabe
Arsenal: Ospina; Bellerin, Mustafi, Koscielny, Monreal; Xhaka, Ramsey, Wilshere, Ozil, Welbeck; Lacazette
Subs: Iwobi, Chambers, Maitland-Niles, Kolasinac, Cech, Nketiah, Mkhitaryan
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