Roberto Mancini will not have been happy seeing his top-four challengers fall to the lowly Tigers, who stormed into a two-goal lead thanks to Jozy Altidore and George Boateng before Emmanuel Adebayor smashed home to set up a frantic finale.
The Citizens failed to get back into the game and they sit sixth in the Premier League table with Liverpool and Tottenham Hotspur narrowly ahead of them.
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City new boy Patrick Vieira made his long-awaited debut and, after coming off the bench, it took him just 17 minutes to receive a yellow card.
Owen Coyle's Bolton side grabbed a goalless draw at home to Fulham but it could have been so different if Mark Clattenburg hadn't ruled out Kevin Davies' last-gasp header.
There appeared to be very little contact inside the penalty area but the whistler disallowed his effort.
The Trotters have a test on their hands if they are to grab a positive result from the City of Manchester Stadium clash.
Mancini's men boast a formidable home record, winning eight and drawing three of their 11 games so far this term in the league.
On the other hand, Bolton have secured just two wins on the road and they sit just one point outside the relegation places.
Big-spending City will be without Roque Santa Cruz and Micah Richards (both calf), Vincent Kompany (groin) and long-term absentee Michael Johnson (knee).
Joleon Lescott is not far away from a first-team return following his own knee injury.
Croatia striker Ivan Klasnic is missing for the visitors with a calf complaint and knee victims Sean Davis and Joey O'Brien will be out of action for some time.