The hosts had their impeccable home form book blotted in the first half when Steven MacLean breached the Britannia stronghold for only the fifth time this season before Burton condemned their play-off exile.
The home side had occupied a much contested fourth spot before only their second defeat at home this term saw them slip four places and out of promotion contention.
Mamady Sidibe's strike looked to have clawed a point back for the hosts before Burton pounced to give Wednesday their third win on the bounce away from home.
Despite a glut of endeavour billowing around in the opening half, neither side looked capable of unlocking the cautious approach of the opposition.
The home side began the bout with five successive clean sheets to their name on home territory and early indications signalled a sixth was imminent.
Wayne Andrews ballooned a shot early on while some stout defending from Danny Higginbotham kept the Wednesday threat at bay.
The defender flung himself into the firing line to charge down MacLean's goal-bound volley before the striker eventually claimed his bounty.
The Scot duly stroked Andrews' pin-point centre into the uncharacteristically gaping net to conclude 546 impervious minutes at the Britannia Stadium.
A 35th minute fracas between Andrews and Lee Hendrie earned each party a caution, however, a graver punishment could have been dealt to the Owls winger when he appeared to have struck Hendrie's face.
After the break it was evident that the blow had made little impact on the Aston Villa loanee's vision when he helped restore parity on the 59th minute.
Sidibe sent a looping header over the rooted Mark Crossley after getting on the end of a deep cross from Hendrie.
But the towering frontman's third strike of the campaign stood for nothing eight minutes later when a former Potter crashed home the winner.
Steve Simonsen's sturdy palms kept out Marcus Tudgay's rocket but, when City's rearguard failed to rid the danger, Burton struck.
The Jamaica striker, who scored twice for City in a brief loan spell in 2002, picked out Simonsen's bottom right-hand corner with some ease to leave City's impeccable home form in tatters.