The Trotters were enduring their worst start to a league season in 111 years having failed to win any of their opening 10 matches, one of only five teams in England's top four divisions still chasing their first success.
But that changed at St Andrew's as they held strong to claim a narrow 2-1 victory against a Blues side who were chasing a fourth successive triumph on home soil for the first time since 2007.
Beckford headed against the crossbar from close range after the interval before former City midfielder Neil Danns capitalised on another glaring error, this time goalkeeper Darren Randolph flapping at Liam Feeney's cross.
Fit-again substitute Nikola Zigic gave Birmingham hope when he headed home his first goal of the season but their rally failed to produce an equaliser, with a late handball appeal against Feeney waved away.
It meant Bolton were left to celebrate heading into the international break, with their mere 375 fans in attendance enjoying a rare victorious trip back up the M6.
No sooner had David Murphy's free-kick tested Bolton goalkeeper Adam Bogdan with the game's first effort than the visitors countered immediately to break the deadlock.
Medo launched a hopeful clearance which Burn, just inside his own half, completely misjudged, allowing Beckford to get in behind and sprint clear before slotting calmly past Randolph.
Chris Burke, as has so often been the case this season, was Birmingham's liveliest outlet and his teasing ball fizzed across the face of goal.
Bogdan dived full stretch to his left in the 40th minute to keep out Callum Reilly's goalbound effort from long range, preserving Bolton's half-time advantage.
Birmingham again quickly imposed their territorial dominance at the start of the second half but once more it was the visitors who posed the biggest threat, this time 11 minutes into the half.
Feeney sent in a right-wing cross and Beckford, having again lost Burn, headed straight against the crossbar from six yards when he really should have scored.
Blues boss Lee Clark turned to Zigic and Lee Novak in a bid to get his side firing, and it immediately added extra impetus.
However, the Blues bubble burst when Randolph failed to collect Feeney's routine cross, allowing Danns to tap home from close range.
The home side immediately gave themselves hope as Zigic made his presence felt, connecting with Burke's deep free-kick to send a looping header over Bogdan.
Blues pressed in search of a leveller but failed to really trouble the Wanderers stopper, with Reilly's penalty appeals for handball against Feeney dismissed.