Elmander and Kevin Davies had twice given Wanderers the lead only for goals from Cameron Jerome and Kevin Phillips to pull Alex McLeish’s team level at St Andrew’s.
But South Korean substitute Lee Chung-Yong had the final say with hit a 90th-minute winner as Bolton booked their first FA Cup semi-final appearance since 1975 with the 3-2 quarter-final win.
With his squad severely depleted by injuries, McLeish could name only six substitutes, but the Birmingham manager was able to call on Barry Ferguson after the midfielder agreed to take a pain-killing injection to play with a broken rib.
It took 13 minutes for the game’s first chance to arrive with Birmingham defender Curtis Davies’ looping header saved comfortably by Trotters goalkeeper Jussi Jaaskelainen from Sebastian Larsson’s free-kick.
Yet eight minutes later it was Bolton who took the lead when Fabrice Muamba overpowered Ferguson to head goalwards, Ivan Klasnic hooked the ball on and
Sweden international Elmander fired inside the left post for his first goal since January 8th.
McLeish’s frustrations grew further when Martin Jiranek, who took an early knock to the ankle, and Ferguson, with what looked to be his thigh, were both forced off with injuries inside the opening half hour with Liam Ridgewell, himself not fully fit, and Nathan Redmond, who only turned 17 last week, brought on.
Yet just as the momentum appeared fully in Bolton’s favour, Birmingham demonstrated their famous fighting spirit thanks to a fine goal to level things up from Jerome seven minutes before half-time.
Jerome’s header into the box was cleared straight back to him by David Wheater and he punished Jussi Jaaskelainen’s poor positioning with a crisp half-volley inside the near post.
Coyle had to be spoken to by referee Phil Dowd in the 54th minute for his furious reaction to his side having a free-kick awarded to them, as opposed to being handed a penalty, when Curtis Davies handballed inside the penalty area under pressure from Gary Cahill.
Four minutes later the officials had another big call to make when Jean Beausejour sent Jerome clean through from the right channel only for Jaaskelainen to dart off his line and send him tumbling, however the Finland goalkeeper took the ball before the man.
Lee made a vital clearance off the line to deny Kevin Phillips with his first touch and it proved a crucial moment as within minutes Bolton had regained the lead.
Curtis Davies clumsily bundled Kevin Davies over inside the area and the Trotters skipper made no mistake with his 66th-minute penalty down the middle.
Jaaskelainen made an outstanding finger-tip save to turn Phillips’ well-struck effort onto the far post four minutes later as the home side pushed for an equaliser.
However, there was nothing he could do about the veteran striker’s stunning hooked effort into the top corner from 22 yards with 10 minutes to go, which had looked set to force a replay until Lee’s dramatic headed winner from a Kevin Davies knock-down.