The Gunners lead the Spanish giants 3-0 from their first leg following two spectacular free-kicks from Declan Rice, and Mikel Merino strike.
Ghana midfielder Thomas Partey played the full minutes of that tie but has since become an injury doubt after picking up a knock in the 1-1 Premier League draw with Brentford on Saturday.
He was replaced by Jurrien Timber after 69 minutes at the Emirates with Arsenal leading 1-0.
Arsenal manager Mikel Arteta said in his post-match interview: "Thomas Partey felt something so we didn't want to take any risks.
"We don't know (the extent of the injury) I haven't spoken to the doctors yet."
Arteta added that Ben White remains sidelined for an undetermined amount of time.
"Ben White, we don't know. He wasn't in condition to make the squad today to be selected. We have a few days so let's wait and see," he said.