The Gunners surrendered a lead for the second time in a week as second-half goals from Leroy Sane and Raheem Sterling transformed a tight Premier League clash after Theo Walcott had struck early.
The Londoners' loss came on the back of a similar reverse at Everton and, as at Goodison Park, Wenger found fault with the officials.
"We conceded two offside goals which is very difficult to accept in a game of that stature," said Wenger
"But, as it is well known, the referees are protected very well like the lions in the zoo, so we have to live with those decisions."
Replays suggested Sane may have been marginally offside as he cancelled out Walcott's fifth-minute opener early in the second half while Wenger also thought David Silva interfered as Sterling struck his 71st-minute winner.
Asked to clarify his remarks concerning referee Martin Atkinson, Wenger said: "I want them to be very well protected, I want them to be safe, but if they could make the right decisions it would be even better."
Arsenal goalkeeper Petr Cech, who was beaten at the near post for the second after Sterling cut inside following a sublime crossfield pass from Kevin De Bruyne, also took issue.
Cech told Sky Sports: "There were players in front of the goal so I didn't see the shot and there were people running across
I don't know if one of them was David Silva or not but, as I said, I didn't see the ball because it was behind the players."
The result left Arsenal in fourth, nine points behind leaders Chelsea, while City moved two points ahead of the Gunners and up to second in the table.
City were lethargic before the break but their rejuvenated display in the second half, in which De Bruyne also hit the post, represented a welcome return to form.
Pep Guardiola's men have failed to match the standards they set during an impressive 10-game winning start to the campaign of late
After the midweek defeat of Watford, the win was only their second at home in the league in three months after a series of frustrating results.
Guardiola said: "Of course it means a lot to win against one of the best teams in the Premier League, Arsenal, after a good comeback.
"We were unlucky in the first minutes when they scored the first goal, they were lucky.
"It was a good game
I think we dominated, like what we are looking for
The victories give a lot of confidence in the mind of the players in what we are trying to do."
Source : PA
Source: PA