The Gunners went into the second leg against BATE Borisov needing to complete a comeback following a surprise 1-0 defeat in Belarus last week.
They responded well and won 3-0 courtesy of a Zakhar Volkov own goal and headers from defensive duo Shkodran Mustafi and Sokratis Papastathopoulos.
Emery opted to recall Ozil, having left him at home for the first leg, with the highest-paid player in the club's history relegated to a peripheral role in recent weeks and making just his second start since Boxing Day.
Despite a run of indifferent form, Emery has told Ozil he needs to shake off his minor injuries and illness to be more consistent.
The former Germany international put in a good showing against BATE, playing the full 90 minutes, but Emery said after the game that he cannot guarantee Ozil will stay in the team long term.
"Today he showed what he wants," Emery said. "If he is available, like the last two weeks, we are going to play a lot of matches and maybe sometimes we need him in the starting XI and sometimes on the bench because we have a lot of players to also help us.
"His spirit like today is good and his quality and capacity and combination with some players is good. I think we need every player and today playing Mesut was important and positive."