Wenger put Alex Oxlade-Chamberlain, Emmanuel Frimpong and Francis Coquelin in the starting lineup and brought on Ignasi Miquel, but he was left without reward with his side going down in Greece.
The Gunners lost Andre Santos and Lukasz Fabianksi to injury, with the latter’s replacement, Vito Mannone, at fault for Olympiakos’ second goal scored by David Fuster.
However, Wenger is hopeful that the game will benefit the young players in the future and admits that his side lost out to more determined opponents.
"It was a fantastic experience they realise what intensity that you need at this level and some young players have shown good things," he told reporters.
"But there was a bit of lack of experience and maturity in midfield where you need to hold the ball better when we were under pressure.
"We had the early chances, but Olympiakos played a very committed game and made a good battle.
"We lost too many balls in the first half and overall became a bit insecure.
"We could sense there was something more at stake for Olympiakos than us, and that made a difference."
"Overall Olympiakos deserved to win, but unfortunately for them it is not enough to qualify."
The Greek side looked poised to qualify for the knockout stages of the Champions League but two late goals by Marseille against Dortmund in the other match in the group saw the Ligue 1 side seal second place.
After the match, Olympiakos manager Ernesto Valverde lamented the way his team had just missed out on progressing to the next stage of the competition.
"It was cruel the way we have been left out of the next phase because in the last five minutes we thought Dortmund were winning the game," he told reporters.
"We can't talk about justice in football, just success at the right time. The good thing is we fought until the very last moment."
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