Danny Ings' first goal at Turf Moor was not enough to slow Birmingham's play-off push as a seventh home defeat of the season left the Clarets still battling to escape the bottom half of the table.
Ings followed up his opening goal in Burnley colours at Portsmouth last Saturday with a 73rd-minute equaliser as Eddie Howe's men threatened to stage a successful comeback.
Danny Ings celebrates his first home goal
On another night Ings could have had a hat-trick in an impressive second-half performance which promised to end the Clarets' four-match wait for a home success.
But the sharper finishing belonged to the Blues who led early on through Marlon King and then bagged the points courtesy of Jordan Mutch and David Murphy right at the death to enhance their prospects of an instant Premier League return.
The Clarets' injury-hit squad was stretched to the limits with Martin Paterson and Ben Mee the latest to join the casualty list.
Charlie Austin's hat-trick at Portsmouth not surprisingly earned the striker a re-call to the starting line-up along with Josh McQuoid, with Ross Wallace forced to deputise at left-back.
But Burnley had barely had time to settle when they behind with ten minutes gone.
Towering City striker Nikola Zigic was always likely to be handful in the air and when he flicked on a throw-in from Murphy, King spun away from David Edgar to fire past the unfortunate Lee Grant from 12 yards.
Grant looked as though he had kept King's effort out with a fine save but after making an initial stop with his outstretched right hand the ball bounced up and over the line via the keeper's back.
Kieran Trippier feels the frustration
The Blues had hardly needed to get out of first gear to go in front and it took Burnley almost half an hour to muster a real response.
The left foot of Wallace had threatened from a couple of set-pieces as the Clarets finally began to ask some questions, although it was a corner from Kieran Trippier that gave Edgar a heading chance he could not direct goalwards from Burnley's best opening of a tepid first half.
For all their possession and the probing of ex-Clarets' hero Wade Elliott, the Blues hadn't really hinted at a second goal until three minutes into the second half when King had the chance to put the game beyond Burnley.
Released by Chris Burke's pass, City's top scorer had a free run towards goal but allowed himself to drift wide and then after delaying his shot saw Michael Duff make a timely block.
Burnley countered with a long-range effort from Ings which Boaz Myhill flapped at unconvincingly, but the Clarets were unable to mount any sustained pressure on a City defence comfortably marshalled by former Turf Moor skipper Steve Caldwell.
With virtually no first-team experience on the bench Howe had limited options to try and change things, although with an hour gone he was forced into his first swap with Junior Stanislas replacing Dean Marney after the midfielder's tidy night's work was ended by a bang on the head.
And with Stanislas immediately helping to liven things up, the Clarets almost equalised in spectacular style as they began a determined fightback.
The substitute's dash through the middle was ended by Myhill's clearance but with the keeper out of his goal, Austin pounced to let fly from 45 yards with a volleyed effort which was heading in until Curtis Davies got back to clear from in front of goal.
If that was a let-off for the visitors, they lived even more dangerously with 20 minutes to go when the Clarets twice hit the woodwork.
Again Stanislas was involved as part of an impressive cameo, pulling the ball back for Ings who should have scored but lifted his shot against the bar, Austin heading the rebound against the same piece of wood.
Josh McQuoid goes close
Ings couldn't have asked for a better opportunity to open his Turf Moor account but the striker didn't hide and moments later got his reward his persistence merited.
Stanislas' original cross was blocked but Wallace followed up with the perfect delivery which Ings met at the near post with a powerful header from eight yards which flew past Myhill.
Ings makes it 1-1
The rejuvenated Clarets were good value for their equaliser and looked capable of going on to secure a first home win in four attempts.
But just two minutes later they undid all their hard work when City went back in front, King again getting clear to pull the ball back for Mutch to side-foot into the top corner.
Howe then gave 17-year-old Cameron Howieson his senior debut late on but there was to be no fairytale finish for the young Kiwi as a mistake from Grant two minutes from the end ushered the Blues over the finishing line as he spilled a cross from Mutch and allowed Murphy to tap in the visitors' third.
Ings still had time to reduce the arrears but a wasteful finish in stoppage time, skying the ball over the bar from close range, failed to give the scoreline a more balanced look as the Clarets again suffered a frustrating bout of home sickness.
Burnley: Grant, Trippier, Wallace, Duff, Edgar, McCann, Marney (Stanislas 59), Bartley, Austin, Ings, McQuoid (Howieson 84). Subs: Hewitt, Fletcher, Jensen.
Booked: Duff 87, Wallace 90
Birmingham: Myhill, Murphy, Caldwell, Ramage, Burke, N'Daw, King (Huseklepp 90), Mutch, Elliott, Zigic (Townsend 76), Davies. Subs:, Doyle, Gomis, Redmond.
Booked: Zigic 27, Mutch 40
Referee: Jock Waugh