Gervinho had given the Gunners the lead at the Emirates Stadium before they were undone by the Greeks on the half-time whistle.
"The second half was better than the first. In the first half we were sloppy and we lost a lot of balls. It was not great really," said Vermaelen.
"The most important thing is to win your home games in the Champions League, we have won one away from home too so we hope that we can continue to pick up points."
The win has seen Arsenal move two points clear of Schalke 04 at the top of Group B.