The Gunners won the first leg in Sweden 3-0 and were expected to cruise in the return fixture at Emirates Stadium.
Goals from Hosam Aiesh and Ken Sema in the space of 70 first-half seconds saw Ostersunds threaten to pull off a huge upset.
And although Sead Kolasinac's strike after the break made it 4-2 on aggregate and settled Arsenal's nerves, Wenger offered a damning verdict of his side's attitude.
"We were not at the races in the first half," he told a news conference.
"We were in trouble because we were complacent and not focused. We were open every time we lost the ball and had no ideas with the ball. That's why we were in trouble.
"In the second half, it was much better. Our energy was high and our domination as consistent. Overall we responded very well. We did the job to qualify. That's what you have to keep from the night and that's it."
"We prepared properly, in a serious way, but you have external circumstances," he said.
"The fact that we won the first leg 3-0, the fact that we have another big game on Sunday, the fact that people subconsciously think they just have to turn up to win the game.
"Football doesn't work like that. We played against a good side and it's what you see in the FA Cup. You can be in trouble every time you're not 100 per cent focused.
"I felt in the first half the whole team was not at the level you expect. It was not easy for the defenders because we lost the ball too early and we didn't' screen well when we lost the ball."