Wenger's side were on course for a last 16-berth for the 15th season running on Tuesday after goals from Mikel Arteta, Alexis Sanchez and Alex Oxlade-Chamberlain.
However, Anthony Vanden Borre's brace was followed by a late Aleksandar Mitrovic equaliser as Arsenal were left to lament a sloppy defensive display.
Having seen his side miss out on progression for the time being at least, Wenger was left frustrated by Vanden Borre's first, where the defender appeared offside, but was angered more by his side's slack play.
"The end result is very disappointing. The first goal was offside but there was a bit of a lack of concentration because we thought the job was done," the Frenchman told Sky Sports.
"There was some fatigue and we had problems to finish the game but overall defensively we were poor from first to last.
"When they came to 3-2 you want to secure yourself but we were maybe not cautious enough. Still if you look at goals two and three it's very poor defending.
"I was never completely sure we were not in danger because the whole game we did not defend well."
Arsenal need only a point from their remaining two games to ensure progression, with games against Borussia Dortmund and Galatasaray to come in Group D.
However, Wenger, who acknowledged both frustration and anger at the result, is refusing to take anything for granted in terms of ensuring a last-16 spot.
"It's hugely disappointing. We have to win our next game and see if we have a chance," he added.
"It's likely now [Borussia] Dortmund will win the group and as I said before [the game] our one worry is to qualify.
"I'm confident because one should be enough but it's not done."
