The Gunners reached the last 16 as a 3-0 win at Emirates Stadium took them through 3-1 on aggregate.
Ozil played the full 90 minutes for the first time since December.
Emery said Arsenal will need the German “sometimes in the starting XI and sometimes on the bench”.
“His spirit like today is good and his quality and capacity and combination with some players is good,” said Emery. “I think we need every player, and playing Mesut was important and positive.”
Arsenal winger Alex Iwobi described Ozil as “world class” and said he hoped the 2014 World Cup winner can “keep on playing”.
“We know what Mesut’s like because we see him in training every day,” he told BT Sport.
“We scored three goals as a result of him playing. I know if I make a run he has the vision to find me.”
Trailing 1-0 from the first leg, Arsenal scored inside four minutes when Pierre-Emerick Aubameyang’s cross was turned in by Bate defender Zakhar Volkov.
Centre-back Shkodran Mustafi made it 2-0 before the break with a powerful header following Granit Xhaka’s corner.
Substitute Sokratis Papastathopoulos headed in the third goal after an hour.