Tomas Rosicky gave Wenger's team the lead in the first half in Athens but goals from Giannis Maniatis and Kostas Mitroglou after the break secured victory for the hosts.
The Frenchman rested several key players after the 2-0 loss to Swansea City on Saturday and insisted that he was happy with the contributions of his fringe men, as well as some of the younger members of his squad.
"I think it was an interesting game," Wenger told ITV. "We had a good first half but we dropped physically in the second half because many players are not used to that level. We had two or three chances to score a second goal but didn't manage to do that.
"Some of the younger players did very well for an hour. That is very positive. Rosicky has not played for six months and had a good 45 minutes. I believe we had a positive game. It's not the result we wanted, but overall it was a very encouraging game."
Olympiakos' equaliser came in controversial circumstances after Leonardo Jardim's side were awarded a corner from which Maniatis bundled the ball past Wojciech Szczesny.
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"It was a goal kick, simple as that," he bemoaned. "What a fifth referee is doing behind the line, nobody knows. I don't think it was the right decision but we have to cope with it. After that, they scored a good goal."
The Gunners' current spell of poor form has seen them slip into 10th place in the Premier League table but Wenger would not be drawn on the subject of possible new additions in the January transfer window.
"That's a key question but I cannot answer it directly after a game," he said. "What is important is that we do well until January. We have big games coming up and we need to focus on the players we have to win the games."
The 63-year-old conceded that finishing top of Group B, which was won by Schalke, might have afforded Arsenal a more favourable draw in the upcoming knockout stage.
"We have to wait for the draw but ideally you would want to finish first," he added.