Malaga held a 2-0 lead from the first leg and started this game in similar fashion.
They created numerous chances in the first half. Isco was guilty of squandering a couple of chances before Joaquin dragged a shot wide from inside the box.
Malaga almost found the goal just after half-time, when Jeremy Toulalan fired just over from long range.
The Greek team nearly took the lead themselves 15 minutes later when Lazaros Christodoulopoulos fired his free kick just over the bar.
The Spanish side were comfortable in the end and will be in next Thursday's group stage draw.