The Clarets dug deep to bounce back to winning ways in the Professional Development League as they hung on with 10 men to join Birmingham in pursuit of table-toppers Leeds United.
Left-back Matty Rain was sent off seven minutes into the second half for a second booking as he collected two of the eight yellow cards dished out in a competitive encounter at the Barnfield Training Centre.
That left Steve Stone’s men with well over half an hour to try and protect a two-goal lead given to them in the opening quarter by Marley Blair and a Jordan Cropper penalty.
They conceded once as Cropper inadvertently scored again, turning a cross into his own net to get the Blues back into the game with 22 minutes to go.
But Burnley then defended magnificently and refused to buckle again as they recovered from back-to-back league defeats to move level on points with second-placed Birmingham and five behind northern group leaders Leeds.
The Clarets, who had won their last two games in cup competitions, had started well and should have been in front after just three minutes.
Josh Benson set the tone for his major contribution with a magnificent defence-splitting pass to release Dan Agyei, who failed to beat Blues goalkeeper Zach Jeacock.
But Agyei responded well to that set-back and provided the opening goal for Blair with a superb run from inside his own half before releasing the winger to tuck away his third goal in two games.
Agyei was involved again in a fine move sparked by Mark Howarth but from Agyei’s teasing cross Tunde Bayode couldn’t convert with a difficult chance at the far post.
The Clarets didn’t have long to wait for a second goal, though, as a shove on skipper Anthony Glennon produced a spot-kick which Cropper smashed into the top corner.
The in-form Blues had been allowed few sights of goal at the other end, but two minutes before the break ex-City goalkeeper Adam Legzdins made a fine save to keep out an effort from highly-regarded teenage forward Jude Bellingham.
Legzdins then went on to become a key figure as a calming influence behind the Clarets defence, where Glennon and second-year scholar Bobby Thomas were a commanding presence throughout a one-sided second half.
Rain’s departure for pulling back Olly McCoy was a harsh lesson for the first-year scholar and prompted a re-shuffle with Scott Wilson coming off the bench to bolster Burnley's back line and Blair making way as Agyei filled in on the left flank.
It was then a rearguard action from the Clarets as Birmingham pressed for an equaliser.
Legzdins tipped over a shot from Ryan Stirk and in stoppage time got down to keep out an effort from McCoy.
But with centre-forward Josh Edwards putting a hat-trick of opportunities just wide, Birmingham had only Cropper’s own-goal to show for their pressure as Burnley bravely came through a major test of character to secure a notable win.
Burnley: Legzdins, Cropper, Thomas, Glennon, Rain, Bayode (Chakwana 85), Benson, Howarth (Trialist), Blair (Wilson 57), Harker, Agyei. Substitutes: Stone, Cook.
Birmingham: Jeacock, O’Keeffe, Burke, McGlip, Bajrami, Redmond, McCoy, Stirk, Andrews, Bellingham, Bailey. Substitutes: Forrest, Daws, McLean, Hurst, Baker.
Referee: Lewis Smith