El Hadji Diouf's match-winning goal in the dying seconds of the opening period hoisted Bolton into the top six and brought a UEFA Cup place a step closer.
The Senegalese striker, on a season-long loan from Liverpool, struck his seventh goal of the campaign to earn his side their sixth away victory in the Premiership.
While Bolton had plenty to cheer, City saw their own hopes of bringing European football to Eastlands recede after they crashed to a fifth home league defeat of the campaign.
And with eight players ruled out through injury and suspension, City manager Kevin Keegan has little scope for making changes in his efforts to find a route into the UEFA Cup.
City ought to have taken the lead midway through the opening period when Robbie Fowler blasted his shot over the crossbar with only goalkeeper Jussi Jaaskelainen to beat.
Bolton struck the decisive blow after 44 minutes and 58 seconds when City failed to clear a Bruno N'Gotty free-kick. Stelios Giannakopoulos got behind Danny Mills on the left and squared the ball across the face of goal for Diouf to slot home at the far post ahead of defender David Sommeil.
City brought on Steve McManaman to replace Willo Flood at the break and later introduced Bradley Wright-Phillips and debutant Lee Croft, but to no avail.
Indeed, Bolton ought to have added to their lead and won by a wider margin.
Diouf had an excellent chance to score a second but blazed well wide after doing the hard work by creating a clear-cut opening for himself.
And Kevin Davies also had two glorious goalscoring chances as he forced David James into a fine stop before heading another opportunity just wide.
Yet at the death City almost snatched an unlikely equaliser when Kiki Musampa headed agonisingly wide.