The Gunners captain missed Sunday's win over Sheffield United after coming down with a bout of flu, and while Arteta is hopeful that Aubameyang can be fit for the second leg, his involvement remains shrouded in uncertainty.
Alexandre Lacazette spurned a brilliant opportunity to give the Gunners the lead in the first leg - hitting the bar after being one-on-one with the goalkeeper - but his brace at the weekend took him up to 50 Premier League goals and he is unlikely to be dropped here.
Teenage starlet Gabriel Martinelli shook off his own injury concerns after notching up his first goal of the season at Bramall Lane and will start on the left if Aubameyang is not available, although Bukayo Saka has overcome a thigh problem as well.
Nicolas Pepe chalked up his seventh goal contribution in this season's Europa League with his opener in the first leg and should feature on the right, while Dani Ceballos could move further forward if Emile Smith Rowe and Martin Odegaard - both nursing ankle problems - cannot play, but the former has a chance of featuring.
Ceballos occupying the number 10 role would see Granit Xhaka link up with Thomas Partey in midfield after he was forced to deputise at left-back at Bramall Lane, meaning that Cedric Soares could once again fill in for the absent Kieran Tierney in Prague.
Hector Bellerin and Calum Chambers are competing for the chance to start at right-back, and the Englishman may get the nod after forcing his way into the first XI, while Bellerin's time at the club is supposedly nearing an end.
David Luiz is working his way back from a knee operation, so Rob Holding's spot in defence is safe, but Gabriel Magalhaes will hope to return over Pablo Mari after the Spaniard was trusted from the off at Bramall Lane.
Arsenal possible starting lineup:
Leno; Chambers, Holding, Gabriel, Cedric; Xhaka, Partey; Pepe, Ceballos, Martinelli; Lacazette body check tags ::