With qualification already secure ahead of Tuesday's last Group B tie against Olympiakos, Wenger elected to leave several first-team regulars behind.
But although Tomas Rosicky fired Arsenal ahead after 38 minutes, the Greeks fought back through a controversial effort by Giannis Maniatis and a well-taken strike from substitute Kostas Mitroglou.
Defeat has left Wenger facing more questions about the direction of his team, who have now not won in four games and have also missed out on a top seed for the Champions League last-16 draw.
But Wenger said: "Let's see [what happens in the draw], but for now it is important for us to focus on the [domestic] championship, forget about the Champions League a little bit and get ourselves back in decent form in the championship."
He added: "We need a good Christmas present now (in the draw), but we will see.
"We can get a bad draw or less strong team, but you normally get strong teams through anyway now.
"The disadvantage we have is we play the second game away, but that is not statistically proven to be such a disadvantage."
Arsenal, who were beaten 2-0 by Swansea City at Emirates Stadium last weekend, host fifth-placed West Brom on Saturday.
And Wenger has challenged his team to produce a response, as he said: "It is a good opportunity for us to keep focused, to show strength and unity, that is what you want to do in the next game."
Rosicky had just come back from an injury lay-off and Wenger revealed his second-half substitution was pre-planned.
He said: "He is a bit tight, muscular, but no [new] injury. We will see how we recovers now for Saturday."