Under the caretaker management of Jimmy Phillips, a revitalised Wanderers outfit showed admirable character following Steven Davies' early brace in the Championship clash at the Reebok Stadium on Saturday.
Davies, on only his second start for the Robins, followed up a superb third-minute volley by dispatching a disputed penalty, but goals either side of half-time from Chris Eagles and Jay Spearing levelled things up.
Several chances went begging for Bolton either side of Spearing's equaliser, yet there was still time for Martin Petrov to pop up with a deserved winner in the 82nd minute.
Petrov, Tim Ream and Benik Afobe gained recalls as Phillips made three changes to the Bolton side defeated at Millwall in the final game of Coyle's reign.
Experienced centre-half Stephen McManus was handed a second debut by City after returning on loan from Middlesbrough, while Martyn Woolford and Davies came in for Jody Morris and Ryan Taylor.
It took Davies little time to make an impact. A short corner routine resulted in Stephen Pearson swinging over a cross from the left and the former Tranmere and Derby forward connected with a acrobatic left-footed volley that gave Adam Bogdan no chance.
With their next meaningful attack, the Robins earned a penalty - much to the fury of the home support - when Woolford, running from left to right across the area, tumbled under a challenge from Ream.
Davies stepped up and confidently found the bottom-right corner from 12 yards as Bogdan went the wrong way.
Wanderers skipper Kevin Davies did his best to inspire an immediate comeback; the veteran saw a half-hearted appeal for a spot-kick turned down and also fired over on the turn.
Yet it was Eagles who pulled one back in the 31st minute, drilling a powerful free-kick under the wall to register his sixth goal of the season after he had been felled on the edge of the box.
The hosts continued to improve thereafter, but survived another penalty claim when Sam Baldock's cross appeared to strike Ream on the arm.
Bolton upped the tempo once more at the start of the second half and Mark Davies fired wide from 15 yards before Petrov and Spearing brought routine saves from Tom Heaton.
With the visitors coming under increasing pressure, Heaton reacted sharply to deny Afobe from close range.
City's goalkeeper was powerless, however, when Spearing latched on to a neat through-ball from Kevin Davies and finished coolly.
The provider of Bolton's equaliser almost prodded his side into the lead moments later, and Heaton continued to be kept busy as the whistle approached.
Ultimately, it was to be Petrov who had the final say. The Bulgarian opened up his body to find the far corner after being played in down the right by good link-up play from Eagles and substitute Lee Chung-yong.