Goals from Robin van Persie and Daniel Karbassiyoon gave Arsenal a place in the Carling Cup fourth round.
Van Persie scored on his debut
Van Persie finished off a typically slick Arsenal passing move with a low left-footed shot after good work by midfielder Mathieu Flamini.
Arsenal's second goal was even better, Karbassiyoon picking up Cesc Fabregas's astute pass and then firing in a shot past Ronald Waterreus.
Robbie Fowler's free-kick reduced the deficit, but the response was too late.
Wenger had made 11 changes to the side that lost to Manchester United so controversially on Sunday, once again opting to field an experimental side for Arsenal's Carling Cup campaign.
But with City fielding an almost full-strength side Wenger's youngsters initially struggled and in the first-half it was not until stoppage time that they contrived to produce a shot of genuine menace, as Waterreus saved Fabregas' drilled effort.
After the interval Arsenal were more ambitious as an attacking force with Arturo Lupoli, Jermaine Pennant, and Van Persie all trying their luck with long-range shots.
Quincy Owusu-Abeyie also broke clear down the Arsenal left and crossed for Van Persie, who skied a reasonable chance over the bar.
But the Dutch youngster, who was making his debut, quickly learnt from his mistake and on 78 minutes he finished a sweeping move after Flamini slipped the ball to him.
In stoppage time substitute Karbassiyoon doubled Arsenal's advantage collecting Fabregas's wonderful pass before scoring with another fine left-footed finish.
Initially City had concentrated their attacks down their right wing giving another of the Arsenal debutants Sebastian Larsson a torrid opening few minutes.
First Larsson upended Willo Flood and then the young Irishman released Wright-Phillips, who scampered away down the City right flank.
The England international crossed to the near post but Robbie Fowler was just unable to reach the ball.
Just before the hour in an almost identical move Fowler nearly got to another Wright-Phillips cross but Justin Hoyte was alert to the danger and cleared the ball for a corner.
Wright-Phillips continued to provide City with plenty of attacking impetus, dribbling his way into the Arsenal box and soon after unleashing a shot Manuel Almunia gratefully clutched to his chest.
Arsenal also had problems tracking Antoine Sibierski's clever runs from midfield and the former Lens midfielder's headed pass almost released Fowler.
Just before the interval Siberski drew a fine save from Almunia with a powerful diving header.
City eventually did manage to find the net, Fowler scoring from a free-kick, even though he slipped as hit the ball.
Man City: Waterreus, Thatcher, Distin, Mills, Onuoha, Flood, D'Laryea (Bradley Wright-Phillips 79), Sibierski, Sinclair (Negouai 69), Shaun Wright-Phillips, Fowler, Negouai (Jordan 83). Subs Not Used: Stuhr-Ellegaard, McCarthy.
Goals: Fowler 90.
Arsenal: Almunia, Hoyte, Cygan, Senderos, Larsson, Pennant (Djourou 89), Fabregas, Flamini, Smith (Owusu-Abeyie 61), Van Persie, Lupoli (Karbassiyoon 82). Subs Not Used: Taylor, Cregg.
Goals: Van Persie 78, Karbassiyoon 90.
Ref: P Walton (Northamptonshire).