Ondrej Kudela missed the first leg through illness and a provisional one-match ban, but the 34-year-old has now been handed a 10-match suspension after being found guilty of racist behaviour towards Rangers' Glen Kamara.
With Simon Deli out after contracting coronavirus and David Hovorka nursing a knee problem, Trpisovsky's one fit centre-back - David Zima - is likely to be partnered by Tomas Holes, who scrambled home a last-gasp equaliser in the first leg.
Holes also found the back of the net from midfield in the weekend's win over Sparta, but he is sure to drop back into defence with Taras Kacharaba ineligible for the Europa League, while Alexander Bah will hope to return at right-back in place of Lukas Masopust.
Unsurprisingly, Trpisovsky made some alterations to the engine room for the weekend, so Jakub Hromada should return over Ondrej Lingr to provide some much-needed defensive stability against a Gunners side vying for goals.
The Czech giants were also without attacking duo Peter Olayinka and Abdallah Sima for the derby win over Sparta, with the club stating that the pair missed out doe to "health problems", but Trpisovsky will hope to welcome both men back for the second leg.
Slavia Prague possible starting lineup:
Kolar; Bah, Holes, Zima, Boril; Hromada, Provod, Stanciu; Dorley, Sima, Olayinka