The Gunners sold the Dutch striker to Manchester United last summer and it looked a costly decision when they dropped to 10th place in the Premier League.
Arsenal looked out of top-four contention when they lost to Tottenham in March, but a superb late run of form has hauled them back above their north London rivals and they could yet snatch third place from Chelsea should other results go their way on Sunday.
Wenger said: "This team suffered for a very long time from a lack of confidence because you take the talisman away - Robin van Persie - and get the new players in, then you lose the first big games and suddenly we are faced with scepticism around the team. You could see that.
"That was the problem and balancing the team took a while, to find a formula to have a good balance in the team. Since this has been back, we have been very efficient.
"The Bayern Munich away game was very important, you could feel after that we could do it, that helped.
"I never felt this team lacked focus or desire to do well, but we lacked confidence for a while."
Wenger added: "The resources are there mentally and physically. We have played for a long time under pressure now, so let's just finish the job."