A goal apiece from the defender and midfielder before half-time were sufficient to see the Premier League title winners take pre-season victory over the north Londoners
A five-minute blitz before half-time was enough to clinch the win for Roberto Mancini's men as first Pablo Zabaleta and then the superb Yaya Toure scored from well-crafted team moves.
The result was a little harsh on Arsenal, who despite only playing their second game of pre-season, looked creative and dangerous in attack without an end product and defensive deficiencies ultimately costing them dearly.
But City looked solid throughout and should justifiably be installed as favourites to reclaim their Premiership title once the new season kicks off on August 18.
Despite the match being a pre-season friendly, both managers named strong starting line-ups as they looked to give their senior players a run out ahead of the new season.
City had endured a mixed pre-season with a win, draw and loss in their three matches and Mancini made only two changes to the side that swept aside Turkish club Besiktas last Friday, with Stefan Savic and Nir Biton replacing Marcos Lopes and Adam Johnson in the City midfield.
Arsene Wenger made four changes to the team that started against a Malaysia XI on Tuesday. Lukas Fabianski, Kyle Bartley, Alex Song and Theo Walcott were all given a chance to impress in place of Vito Mannone, Johan Djourou, Francis Coquelin and Marouane Chamakh, who were dropped to the bench.
With three pre-season games already under their belt, it was of little surprise that Manchester City started the stronger, testing Arsenal down the flanks with Carloz Tevez looking particularly sprightly, forcing Fabianski into an early routine save.
The Gunners, however, began to settle into their metronomic passing rhythm and the pace of their front three on the counter attack was making for a lively encounter with Walcott seeing a shot blocked by Kolo Toure after an impressive Gervinho run.
Shortly after, Carl Jenkinson's 20-yard drive was pushed behind by Costel Pantilimon and from the resulting corner, Andre Santos' delicious curling effort flashed inches wide of the Romanian's post as Arsenal started to get a foothold on proceedings.
City continued to test the Arsenal offside trap though, and Aguero was prevented from opening the scoring by a last ditch Jenkinson block with the game becoming more and more stretched.
As the half wore on, it was Arsenal who were looking the more likely to break the deadlock, and from another rapid counter attack Walcott was unfortunate to see his 25 yard effort bend past the post, with Pantilimon beaten, before Jenkinson saw another long range drive fly over.
Pantilimon was certainly the busier of the two keepers and had to be alert once more to palm behind an Andre Santos drive while Aguero should have done better at the other end than to blaze over after a trademark bustling run from Yaya Toure.
It was largely against the run of play that City took a 41st minute lead. Yaya Toure again was instrumental in the move as he shimmied on the edge of the area before sliding a perfectly weighted pass to the overlapping Pablo Zabaleta who smashed the ball past Fabianski.
And the Premier League champions took advantage of further hesitancy in the Arsenal defence to double their lead on the stroke of half time. Questions could be asked of the Gunners fullbacks once more, as Kolarov had time and space to pick out a cross which eventually fell to the influential Yaya Toure to poke home from six yards out.
As is customary in pre-season, Arsenal made 4 half time changes, withdrawing Diaby, Walcott, Bartley and Arteta in favour of Alex Oxlade-Chamberlain, Marouane Chamakh, Francis Coquelin and Ignasi Miquel.
City opted to stick with their starting eleven and seemed content to sit back and let Arsenal play in front of them, a tactic that almost proved costly in the 49th minute as Gervinho forced a good stop from Pantilimon after a flowing Gunners move.
The north Londoners continued their bright start to the second half with sub Oxlade-Chamberlain unfortunate to see his 25 yard fizzing shot rebound off both posts, with Kieran Gibbs; follow up deflected over.
With Arsenal committing so many men forward though, their defence looked vulnerable on the counter attack and after a fine Tevez burst, Aguero should have done better than to clip the ball wide from 10 yards out.
City keeper Pantilimon continued to be sporadically tested in appalling conditions, having to be alert to push away long range efforts from impressive substitute Chuks Aneke and Gibbs.
And further slick build up play resulted in more Arsenal prolifigacy as Craig Eastmond fired wide after a lovely flick by Chamakh.
But Arsenal weren't to be rewarded for their excellent second half display and City closed out the win in relative comfort to underline their credentials ahead of their Premier League defence.