Both goals came in the final five minutes of the first half, the opener coming courtesy of Pablo Zabaleta followed by a close-range strike from Yaya Toure.
Although technically a friendly, the match was surrounded by plenty of hostility off the pitch. Manchester City are actively pursuing Gunners captain Robin van Persie this summer, a move that would add to the list of names that have joined City from Arsene Wenger's side.
Last summer Samir Nasri and Gael Clichy moved North, following similar deals for Emmanuel Adebayor and Kolo Toure.
With Van Persie left at home, Arsenal began with Gervinho up front, while City called upon the impressive Argentine duo of Carlos Tevez and Sergio Aguero.
It was one of City's unheralded starters that created the opening for the first goal. Israeli trialist Nir Briton got forward down the left before laying it square to Toure on the edge of the box, who passed it on for the fast arriving Pablo Zabaleta to produce a fine finish across Lukasz Fabianski in the Arsenal goal.
Toure went from provider to scorer less than four minutes later as Arsenal's defense suffered another all-too-familiar lapse. It was down the left where the damage was done once again. Aleksandar Kolarov made a recognizable surge forward from left-back before feeding Aguero who scuffed the ball back across the face of goal where Toure reacted to prod home from just a couple of yards out.
As rain poured down at the "Bird's Nest" Stadium, the second-half failed to produce further goals. Both sides gained valuable fitness, but City should also receive a welcome confidence boost as they prepare for the defense of their Premier League title.
Manchester City continue their pre-season with a trip to take on Malaysia on Monday, while Arsenal will travel to Hong Kong to take on Kitchee FC in two days' time.