The trio, as well as full-back Sead Kolasinac, missed Sunday's 4-1 Premier League win over West Ham with minor complaints, but all were part of the squad working at London Colney at Wednesday.
Ozil was ill, while Cech had a minor hip injury as Wilshere and Kolasinac were sidelined with ankle problems.
Mohamed Elneny was carried off on a stretcher on the stroke of half-time with ankle ligament damage, although Arsenal are hopeful he will play again this season.
Henrikh Mkhitaryan is also absent, but could feature in the second leg in Madrid next week, having trained away from the group on Wednesday.
The returning trio are a major boost to outgoing Arsenal boss Arsene Wenger as he looks to end his near-22 year tenure with a European trophy.
Although Atletico themselves were given good news as former Chelsea forward Diego Costa was passed fit to travel to London following a hamstring injury.
The former Chelsea man picked up a hamstring injury during the quarter-final second leg clash at Sporting Lisbon.
Atletico boss Diego Simeone had raised Arsenal hopes that he would be out after earlier saying: "The doctors will inform us but I think it won't be possible for him to be ready for Thursday game.
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"He will be for sure in the return leg, but I think he has no chances to be in the first leg."
Costa is unpopular with Arsenal fans for his role in Gabriel Paulista's red card in a 2015 clash which Chelsea won 2-0.
The Spaniard scored three goals against the Gunners during his three years in English football, including a winner at the Emirates in 2016.
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