The Blues went into the game unbeaten in their three previous MSC matches this season having beaten Stockport, Oldham and Bury, but found themselves behind after just 12 minutes.
It was Bolton’s first attack of any real note and poor defending left Nedum Onuoha somewhat exposed with a two-v-one situation in the visitors’ favour.
Portuguese striker Ricardo Vaz Te drew the City defender in and then played in the unmarked Sam Sheridan who made no mistake from eight yards out.
The Blues responded well with Alex Nimely striking the post on 16 minutes and Ben Mee saw a glancing header go inches wide a minute later. The lively Nimely was a constant threat and came close to levelling twice more before the break.
Within four minutes of the second half, however, City finally levelled matters when Robbie Mak was brought down in the box and Andrew Tutte stepped up to slot home his second penalty in as many games.
Both keepers then kept their team in the game, firstly when City’s Tobias Johansen denied Zoltan Harsanyi and then Bolton’s Rob Lainton made two fines saves in succession, the latter denying Dedryck Boyata from point-blank range.
With no further goals during normal time and the score tied at 1-1, the game went to penalties.
Bolton scored all five of their spot-kicks, but while Tutte, James Poole, Greg Cunningham and Robbie Mak scored City’s first four, Kieran Trippier saw his effort saved to hand the visitors victory.