After a three-game barren spell in front of goal, England starlets David Bentley and Matt Derbyshire handed Rovers a deserved two-goal lead, before Roque Santa Cruz made the tie safe in time added on.
Swedish left-back Martin Olsson was handed his full debut by manager Mark Hughes, who made five changes to the Rovers line-up that lost 2-0 to Portsmouth at Ewood Park just three days earlier.
Steve Bruce, meanwhile, named a completely different starting eleven to the side that held Liverpool to a goalless draw at the weekend - a team that included three former Rovers trainees, Martin Taylor, Neil Danns and captain Damien Johnson.
Eager to bounce back from successive defeats, Rovers attacked from the off. On two minutes, Bentley curled a free-kick just inches over the bar, before Derbyshire saw two efforts cleared off the line. In between, Derbyshire's ball in struck Jason Roberts and Richard Kingson pulled off a superb reaction save.
Roberts ought to have opened the scoring from a Bentley corner moments later, but after mistiming his header, the ball flashed across an unsuspecting Derbyshire in front of goal.
After skipping past two defenders, former Blues midfielder David Dunn forced a smart save from Kingson on 25 minutes, before the impressive Christopher Samba headed over the bar from another Bentley set-piece.
A minute later, Bentley and Roberts played a neat one-two inside the box, but neither was able to get a shot away. Straight up the other end, Mikael Forssell broke quickly into the Rovers box and when strike partner Gary O'Connor stole the ball off his toes, Brad Friedel was forced into a superb diving save.
Rovers best chance of the half arrived on 37 minutes when Bentley played Derbyshire clean through on goal, but the England Under-21 striker's shot deflected off the legs of Kingson and over the bar.
Three minutes later, Samba challenged Kingson from a Bentley free-kick, but as the keeper made the save, he collided with the up-right and evidently looked in trouble when he hit the ground. After initially receiving treatment, the Ghanaian collapsed inside his six-yard box and was carefully stretchered off to be replaced by Colin Doyle.
The substitute keeper's first port of call was almost to pick the ball out of his own net, as six minutes into stoppage time, Dunn's left-foot strike curled agonisingly wide of the far post.
Rovers started the second half in much the same vein. A Dunn free-kick appeared to strike the arm of a Birmingham player in the wall, but appeals for a penalty were waved away.
Roberts was then played clean through by Bentley, but after curling his effort just wide of the post, the Grenada international twisted and landed awkwardly, and was subsequently substituted for Santa Cruz.
On 59 minutes, Samba advanced from midfield before letting fly from long range, Doyle spilled the shot and Derbyshire somehow hit the bar with the goal at his mercy.
On 65 minutes, Rovers eventually broke the deadlock in spectacular style, when Bentley smashed home a superb solo strike from 25 yards.
On 68 minutes, Danns saw a shot comfortably saved by Friedel and ten minutes later, a ball into Santa Cruz was headed into the path of Dunn, but the Blackburn-born midfielder couldn't slot past the keeper.
A minute later, substitute Rafael Schmitz held back the run of Derbyshire inside the box and the young Rovers striker stepped up to calmly slot home from the spot.
Santa Cruz almost added the third with a neat flick from substitute Stephen Warnock's excellent cross on 84 minutes, but as the clock ticked past 90, the former Bayern Munich marksman did open his goalscoring account at Ewood Park, with a neat header from Brett Emerton's deflected shot.