City dominated the game and created the best chances but were unable to see off the Trotters and the game finished 1-1.
The visitors even took the lead with their only real chance of the game with Dale Whitehead heading home at the far post from Reda Kribib’s left-wing cross.
Earlier Bradley Wright-Phillips sent a rebound wide following a mazy run from Willo Flood, and was then denied by keeper Andy Oakes after a pass by Marc Lairds.
Christian Negouai and Micah Richards, in his first full appearance for the reserves, both went close as City pressed forward for an equaliser, before Flood's rasping shot was saved.
But after 65 minutes, Bolton committed a pushing offence in their own box and Wright-Phillips scored from the spot.
The new senior player then flashed a header wide from a cross by Flood, whose late free-kick was saved by Oakes to guarantee penalties. Flood, Collins and Onuoha scored for the Blues, but McCarthy and Wright-Phillips were unsuccessful. Fadiga, Campo, Platt and Luisi all scored for Bolton to give them the win.
City: Weaver, Lee-Matthews, Collins, Negouai, McCarthy, Onuoha, Flood, Richards, Bermingham, Wright-Phillips, Laird.
Subs: Schmeichel (GK), Warrender, N D’Laryea, Bennett, Miller.
Attendance: 297.