The FA decided to take no action against Manchester City midfielder Yaya Toure for an apparent kick at Norwich's Ricky van Wolfswinkel during the closing stages of Saturday's goalless draw at Carrow Road, an incident which was missed by the match officials.
Chelsea manager Jose Mourinho, who views City as the title favourites, claimed not suspending Toure sent out the wrong message.
Wenger accepts the decisions of the independent panel may in some cases be difficult to understand, but believes in what they stand for.
"It is a decision we have to accept," said Wenger, whose side were knocked off the top of the Barclays Premier League by Chelsea after they were thrashed 5-1 at Liverpool.
"This decision is questioned, and people who make these decisions can answer these questions, I do not know why they made the decision.
"One positive thing is that this committee exists and that the players know that they can be punished even after the game, so that is very positive.
"After that, the decision is made by human beings and then you have to accept we will not always agree on the way the decisions are made.
"But it is a good thing that this committee and the whole (disciplinary) process exists."
The decision not to take action against the Ivory Coast star is a huge boost for City - he could have faced a three-match ban but the three-man panel of former elite referees which reviewed the incident did not unanimously believe it was an act of violent conduct.
That will come as a big relief to City boss Manuel Pellegrini as his club chase the Premier League and FA Cup trophies - including a home match against Chelsea in the cup this weekend.
Blues boss Mourinho, though, was less than impressed.
"If he is not suspended, the message is clear: the players can do what they want if the referee doesn't see," he said ahead of the panel's decision being made on Monday afternoon.
"If there's no suspension, the message is normally that, if the FA defends football, he'd have to be suspended.
"It's the same for everyone: if the referee doesn't see, I can do whatever.
"It doesn't matter about cameras or others seeing. I can do whatever I want."
Toure, arguably City's most influential player this season, will now be available for Wednesday's game against Sunderland, the Chelsea cup tie and the league fixture against Stoke.
Norwich boss Chris Hughton, meanwhile, claimed Toure did kick his player, though said it was a "minimal incident".
Van Wolfswinkel also gave his backing to the decision, writing on Twitter: "Good to see Toure not getting suspended. Players like him belong on the pitch! What happens at Carrow Road stays at Carrow Road.
"Things happen on the pitch. But we all enjoy watching him play. So get on with it and enjoy the football. That's what it's all about."
There was more good news for City on Monday, with Sergio Aguero and Samir Nasri taking part in a training session after injuries.