Talented teenager Marcos Lopes opened the scoring with forward Stevan Jovetic doubling the lead and Jordi Hiwula wrapping up a 3-0 result with a late penalty.
Manuel Pellegrini named a strong starting line-up, with the likes of Aleksandar Kolarov, Gael Clichy, Javi Garcia, Samir Nasri and Jovetic all starting for the Barclays Premier League champions in the Hazza Bin Zayed Stadium.
City's first chance came as captain for the night Kolarov fired an effort wide before Lopes' low shot was pushed behind for a corner.
The game was being played at a slow pace as Al Ain made mass substitutions midway through the half, with Micah Richards striking a post on 33 minutes as the visitors struggled to impose themselves on the game.
Nasri, who was not included in France's World Cup squad, should have done better with a chance before the break but he could only turn Kolarov's cross over the bar as the first half ended goalless.
Richard Wright was introduced at the interval and he was forced into a smart save at his near post before Shehab Ahmed bent a free-kick just wide as the hosts started the second half brightly.
City then started to show their cutting edge as they broke forward with Jovetic, who bent an effort inches wide of the target before they went ahead shortly afterwards as Lopes timed his run to perfection to latch on to Nasri's through-ball and finish with aplomb.
The highly-rated 18-year-old was not as clinical moments later when he could only place a Kolarov cross wide from close range.
Wright was on hand to keep City in front with a great double-save before Dedryck Boyata burst through the Al Ain defence only to fire his shot over the crossbar with the game opening up in the final 20 minutes.
The game was ended as a contest as Jovetic showed good composure before firing in City's second with a little over 10 minutes remaining, with substitute Sinan Bytyqi wasting a fine chance to add a third.
It was fellow substitute and youth team player Hiwula who scored from the spot in the final minute after he had been upended to win a penalty.