And on a day to forget for Wenger's men, midfielder Jack Wilshere was facing possible censure after appearing to make a crude gesture to home fans during the second half at the Etihad Stadium.
The Gunners struggled to handle the hosts' attacking threat but Wenger claimed his side were still the equal of City, despite the clear implications of the result in title terms.
Wenger said: "It was a difficult game. We had the best defence in the league and we conceded many goals today.
"Honestly, we could have scored at least six as well, it was a very open game.
"I think we made too many mistakes. Our strength until now was our defensive discipline but that went as the game went on.
"We were in a position where we could see the legs were tired a little bit and we had to run after the score.
"What hurts me more was that we had the opportunity to put Man City at nine points and now they are three points (behind).
"That is very different. That is a team that was not unbeatable today."
In a moment of controversy, Wilshere was caught on camera gesturing towards supporters.
The matter could be looked at by the Football Association, who will await referee Martin Atkinson's report.
Wenger said: "I didn't see that. I don't know if he did it. If he did it and is banned, we will have to accept it."
Playmaker Mesut Ozil also appeared to head for the dressing room straight after the final whistle without joining his team-mates to applaud the visiting fans.
An argument with fellow German Per Mertesacker reportedly ensured but Wenger played down the incident.
He said: "That is the Germans, they will sort that out between themselves. Don't worry."
Arsenal had gone into the Saturday lunchtime game at a perceived disadvantage after playing in the Champions League on Wednesday night, 24 hours after City had been in action.
But Wenger said: "I don't want to look for excuses after a defeat like that but it doesn't help.
"I said before the game I would not use it as an excuse and I won't do it now, but it was not ideal.
"You could see we were not as fresh as we should be for a big game."
City's victory, which maintained their 100 per cent home record in some style, is certain to see their status as title favourites strengthened but Wenger did not necessarily agree.
He said: "They are one of the teams to beat, but not more than any of the other ones we have played until now.
"We have played Everton, who were as good as City, and Southampton, who were as good as City."
City's prolific strikeforce of Sergio Aguero and Alvaro Negredo put them ahead before Fernandinho struck twice and David Silva and Yaya Toure also scored.
Arsenal remained in contention for over an hour after two goals from Theo Walcott but Mertesacker's late header was mere consolation.
City have now scored 35 goals in their eight home league games but manager Manuel Pellegrini continues to demand more.
He said: "Today I don't think it was the best performance because Arsenal scored three goals and that is too much for the amount of chances they had.
"But it was a very complete game in attacking. It is not easy to score six goals against Arsenal, the best defence in the Premier League.
"We had at least four or five more clear chances to score goals. In that sense I am very happy but we must continue improving.
"We are not thinking at the moment title hopes. We have a lot more to fight with six or seven important teams.
"I think we must continue improving."
The downside for City was the loss of top scorer Aguero through injury early in the second half and the Argentinian is now facing a lay-off.
Pellegrini said: "Aguero has a problem in his calf. We will see tomorrow how many weeks he will be out."
Arsenal will also assess defender Laurent Koscielny after he suffered a deep cut to the knee attempting to prevent Negredo scoring.
Wenger said: "He has a cut. He will be out for a while but for how long I don't know."
Source: PA
Source: PA