Rovers go into the international break off the back of a defeat in a close encounter at St. Andrew's.
Stephen Gleeson's solitary second half strike was enough to give the home side all three points on a frustrating afternoon for Owen Coyle's side.
Rovers had the better of the first half with Marvin Emnes, Danny Graham and Tommie Hoban going close for the visitors, Che Adams just wide for Birmingham.
Only an outstanding save from Adam Legzdins at the start of the second half stopped Emnes from giving Rovers the lead, but it was the home side who stepped it up, getting their noses in front just past the hour mark when Gleeson swept home David Cotterill's cross.
But as Rovers struggled to muster a response, Birmingham ended the game strongly. Cotterill striking the foot of the post, before Jason Steele denied Lukas Jutkiewicz.
The final moments saw Rovers threaten from a free-kick, but as Sam Gallagher nodded across the box, keeper Steele couldn't get the vital touch in front of goal.
The first half saw plenty of opportunities for both sides but neither goalkeeper was called upon to make a save.
On nine Rovers pressed when recalled duo Darragh Lenihan and Danny Graham combined to feed Marvin Emnes, the Dutchman raced into the area but just as he was set to pull the trigger, defender Jonathan Spector got back to make the tackle in the nick of time.
David Cotterill was finding plenty of joy on the right for the home side. A free-kick from the Welshman was headed over by Michael Morrison, before the winger fed Stephen Gleeson who fired over from 20-yards.
Emnes then headed over when in front of goal after being picked out by Ben Marshall, whilst at the other end Che Adams fired narrowly wide from the edge of the box.
Rovers pressed for the opening goal in the closing stages of the half as Lenihan and Graham both spurned chances, but it was defender Tommie Hoban with the best opportunity of the 45 but he glanced Craig Conway's free-kick just beyond the far post.
The hosts threatened early in the second half when Jacques Maghoma crossed for Gleeson, but the midfielder fired over from just inside the area. However they were then grateful for a stunning save from Adam Legzdins to keep Rovers at bay.
On 53 minutes the ball arrived at the feet of Emnes and quick as a flash the forward let fly, but the Birmingham keeper flung himself to his right to touch the shot around the post.
However the deadlock was finally broken on 64th minute when the Midlands side took the lead.
The lively Cotterill beat two on the right to cut into the area, and as Corry Evans failed to clear, Gleeson swept the ball home high beyond Steele.
That meant Rovers would have to come from behind once again in a match, but against a Birmingham side that had lost just once this season, and with one of the tightest defences in the division with just nine goals conceded, they found opportunities hard to come by.
Instead it was the home side who posed the greater threat. Ryan Shotton fired straight at Steele from a corner. Then Cotterill lashed a bouncing ball against the foot of the post with Lukas Jutkiewicz denied by the Rovers keeper on the rebound.
After a lengthy delay for a clash of heads, a 99th minute free-kick saw Rovers throw everyone forward, Gallagher nodded Conway's free-kick into the path of Steele but he couldn't claim the vital touch.
BIRMINGHAM: Legzdins, Grounds, Shotton, Gleeson, Cotterill, Adams (sub Fabbrini 63 mins), Jutkiewicz, Maghoma (sub Wiggins 85 mins), Spector, Davis (sub Robinson 90+1 mins), Morrison (c).
Subs not used: Trueman (GK), Brown, Stewart, Storer.
Goals: Gleeson 64 mins.
ROVERS: Steele, Lowe (c), Greer, Hoban, Williams, Marshall, Lenihan, Evans (sub Guthrie 67 mins), Conway, Emnes (sub Bennett 74 mins), Graham (sub Gallagher 55 mins).
Subs not used: Raya (GK), Samuelsen, Akpan, Brown.
Booked: Lowe 21 mins, Lenihan 30 mins, Graham 51 mins, Marshall 68 mins, Guthrie 71 mins, Hoban 81 mins.
Attendance: 16,781 (including 555 Rovers fans)