The Frenchman asked the club's supporters to respect their former hero before the game but says he understands why they still hold a grudge against the Manchester United striker
The Dutchman returned to the Emirates on Sunday and converted a penalty on his old ground to derail the Gunners' push for Champions League qualification.
Before the game a guard of honour formed by Arsenal players for the Premier League champions was greeted by a cacophony of boos from the home crowd, with Van Persie recieving similar treatment with almost every touch of the ball.
"When he was here, he didn't get this kind of reception. They loved him. So today is a bit if disappointed love," Wenger told reporters.
"He's in our dressing room and the moment, because our food is better! You know people who play together for five or six years they fight. Our defenders didn't make it easy for him.
"We are rivals but and the end of the day we decided to sell him. You want us to make a guard of honour and respect the champion, then you have to accept that respect exists after the game.
"When you want to give absolutely everything in the game, after it you can still have respect."
Arsenal got off to the perfect start thanks to Theo Walcott's goal inside two minutes, but Van Persie levelled the scores from 12 yards on the stroke of half-time having been felled by Bacary Sagna.
And Wenger admits the goal his side conceded came at the worst possible time, halting their momentum and disrupting their gameplan.
He continued: "It was a quality game with a lot on intensity. I believe we were on top in the first half and it was a disappointing to concede the equaliser the way we did it.
"Why? Because it put us in the position in the second half were we had to completely open ourselves up. We threw everything forward, sometimes more with energy than technique.
"Overall I can only praise the players for the dynamic, the effort and the desire they put in. Let's keep going like that and we have a chance to be where we want to be.
"I'm convinced we will be there but there is no room for dropping points."
The Gunners boss dismissed suggestions that the guard of honour actually helped his players make that fast start, instead attributing their efforts to mental preparation.
"No[it didn't help us], mental preparation was reason not the guard of honour. If it helps us, I promise you we would do one every week!" he said jokingly.
Sagna's rash challenge on Van Persie led to the penalty which the Dutchman later converted, and afterwards Wenger revealed his right-back was still at a loss to explain what had made him do it.
He added: "No, [he didn't explain why he made that pass], he is very disappointed he is a player who gives absolutely everything in every game.
"I think he made a bad pass, that can happen. After he panicked a little bit and wanted to repair what he did too quickly. He had time to tackle.
"But he has saved us so many times in the past. It's unfortunate what happened to him today."