The result left them as runners up to Schalke in Group B, with the German team claiming a draw away to Montpellier.
With qualification for the final 16 already guaranteed, the Frenchman decided to rest a number of his first-team regulars.
This contributed to the negative score-line, but Wenger was happy with the performances of some of his fringe players:
“Some of the young players did very well for an hour and that’s very positive,” he told SkySports.
“It wasn’t the result we wanted but it was a very encouraging game.”
The display of 20-year-old defender Jernade Meade was singled out by the manager as being particularly impressive:
“He tired late on but he was my pick,”
He was however unhappy at the manner in which his team conceded the equalising goal:
“It was a goal kick, simple as that. What a FIFA official is doing behind the line, nobody knows.
“It’s not the right decision but you have to cope with it. After that they scored a good goal.
Tomas Rosicky opened the scoring for the Londoners, before goals from Ioannis Maniatis and Kostas Mitroglou sealing victory for the Greek side.