A free-kick early in the game from man-of-the-match Aleksander Kolarov gave the champions a perfect start before substitute Sergio Aguero and James Milner secured three points for Roberto Mancini’s side.
Following their 1-1 draw at home to Borussia Dortmund in the Champions League, City boss Mancini made seven changes from the side that took to the field on Wednesday night, most notably with captain Vincent Kompany missing through injury.
It took just five minutes for the Citizens to take the lead after defender Carlos Cuellar, who was in the starting XI at the expense of Titus Bramble, made a rash challenge on Carlos Tevez on the edge of his area.
Kolarov exquisitely curled the set-piece past Simon Mignolet for his first league goal of the season.
From then on in it was all hands to the pump for the Mackems as City continued to push forward looking for that all-important second goal.
It came when Mancini swapped Balotelli for Aguero, with the former clearly unhappy at the decision, ignoring his manager and heading straight for the changing rooms as he trudged off.
Yet the change worked as four minutes after coming on Aguero fired a Kolarov cross past Mignolet before Milner scored from a free kick in the dying embers of the game.