Kevin Nolan grabbed a last-gasp winner for Bolton as Sam Allardyce's side secured their first victory in 11 games.
It was a richly deserved success as Bolton finished strongly while Birmingham alarmingly went off the boil with a very poor defensive performance.
Matt Upson added another bow to his repertoire by scoring his second goal of the season but his equaliser could not save Birmingham from their second successive defeat.
The Robbie Savage controversy may have been the main talking point before the game but Birmingham's performance left a great deal to be desired.
City, as expected, left Savage out of their line-up and at the present time there appears little indication of how the impasse will be solved.
There was no doubt that Birmingham missed the industry of the Welsh international and the injured David Dunn as the midfield lacked drive and this was reflected by Darren Anderton struggling to step into the gap in the first half.
On the other hand there was a real determination about a Bolton side that was extremely keen to atone for their recent slump.
Early on in the game there were ominous warnings for Birmingham's defence when Bolton captain Jay-Jay Okocha struggled to gain control of a short cross from Nolan.
Okocha, to his credit, was not put off by the incident and went on to cause considerable consternation among the Birmingham defenders particularly when he cleverly sent Nolan clear only for the Bolton man to see his low shot pushed away by Maik Taylor.
The live-wire Okocha could not be subdued and the larger than life character, who from the start received an adverse reaction from the home fans, produced a rocket shot which Taylor saved magnificently only for the alert El-Hadji Diouf to turn home the rebound.
Birmingham's response was to produce several disjointed attacks that lacked conviction.
Emile Heskey managed to outpace the Bolton defence but Jussi Jaaskelainen blocked his powerful shot and the Finnish keeper then saved Olivier Tebily's long-range effort.
Referee Uriah Rennie came in for some heated comments from the fans for his long-winded handling of a clash between Heskey and Radhi Jaidi which resulted in both players being booked as Birmingham stepped up the pressure on Bolton's defence.
Aussie Stan Lazaridis was a problem for Bolton as he gained in confidence to carry the ball into the heart of the opposition's penalty area but he was generally thwarted by some dogged rearguard action.
The second period developed into an all-action performance from Birmingham with Bolton dropping back to defend their slender advantage.
Mario Melchiot often moved forward to give Birmingham extra attacking power and went close to an equaliser with a close-range header that dipped just over the bar.
But it spurred Birmingham to greater heights and in the 66th minute Upson moved up for an Anderton corner. The ball found Clinton Morrison with his back to goal but he contrived to produce an overhead kick that cannoned off the post back to Upson who was able to force the ball home from about five yards.
Bolton, however, staged a late rally with Okocha their inspiration as he fired in a last minute shot that rebounded off Taylor to Nolan who notched the winner.