The 20-year-old was omitted entirely for the 4-0 Premier League win over Newcastle on Sunday after a row with manager Mikel Arteta and members of his coaching staff during a recent warm-weather training camp in Dubai.
While Guendouzi looks set to return, Mesut Ozil will miss the last-32, first-leg match at Karaiskakis Stadium due to personal reasons, with his wife due to give birth soon.
Lucas Torreira also did not join his team-mates in making the journey on Wednesday as the result of an illness.
However, the combative Uruguayan international could yet fly out tomorrow if he recovers in time.
January recruit Pablo Mari is available to make his senior Arsenal debut after topping up his fitness with a 45-minute outing for the Under-23s against Chelsea on Monday night.
Arsenal remain without another new signing in Cedric Soares, who is hoping to return to full training by the end of the month after a knee ligament injury.
That is the same case for fellow full-back Kieran Tierney as he works his way back from a dislocated shoulder suffered against West Ham in December.
Defensive colleague Calum Chambers was ruled out for the rest of the season last month after rupturing the anterior cruciate ligament in his left knee.