An open first half produced chances for both sides but neither team took advantage so was 0-0 at half time.
Nigerian star Jay Jay Okocha hit the crossbar for Bolton with a 30 yard screamer before Birmingham took the lead just after the hour when the ball was poorly cleared from a corner and Darren Purse half-volleyed home from outside the area.
Bolton then suffered another blow when Jamaican winger Ricardo Gardner was controversially sent off for a second bookable offence following a tussle with Blues striker Geoff Horsfield.
Wanderers then scored a shock equaliser when Okocha scored a neat volley at the far post. However, Birmingham took the lead barely a minute after the equaliser when, not the first time this season, Bolton fell asleep at the back and Welshman Robbie Savage rounded Jussi Jaaskelainen and slotted home. Horsfield clinched it in the last minute.
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