The Brewers knocked out Aston Villa at the Pirelli Stadium last month to set up this tie with Burnley.
And Nigel Clough’s giant-killers stunned those wearing claret and blue again last night as they came from behind to beat their Premier League visitors.
It looked set to be a routine night for Burnley when Kevin Long headed them in front just before the break.
But Burton hit back in the second half as Liam Boyce scored and then turned provider for Allen, who notched a famous winner seven minutes from time.
It is the first time Clough has won against Premier League opposition as Brewers boss, having lost against Liverpool, Manchester United and Watford by an aggregate score of 1-11.
Yet Burton are the fourth side from League One or lower who have beaten Burnley in the last three years, after Port Vale, Accrington and Lincoln.
This shock result also caps what has been a miserable start to the season for Dyche, who once shared a dressing room with Clough at Nottingham Forest.
The Clarets were knocked out of the Europa League at the qualifying stage.
And they have only won just one of their six Premier League games so far – even if that was a record 4-0 win over Bournemouth at the weekend.
The only comfort Dyche can take from last night’s trip to the Pirelli was the return of key midfielder Steven Defour, who had been out since January following knee surgery.
Tom Heaton was also making his first domestic appearance since he dislocated a shoulder a year ago – and was greeted on to the pitch with cries of “England’s No1” from away fans.
But the fit-again Three Lions international was to have a night to forget.
Heaton had to make one early save through a box of bodies from Scott Fraser after a Jake Hesketh cross.
At the other end, just seconds later, Chris Wood steered wide a chance he should have buried from McNeil’s cross.
And though he did soon have the ball in the net, the New Zealander was flagged offside.
Long suffered the same fate soon after when he controlled and fired in from Defour’s chip.
But Burnley and Long did get one stand on 40 minutes, as the Ireland centre-half rose highest to head home Johann Berg Gudmundsson’s corner for just his third goal in eight years at the club.
Still, after a half-time talking to from Clough, the Brewers started the second half strongly.
And David Templeton gave Heaton a scare when he cut in from the left and curled just wide.
Gudmundsson should have put the tie to bed for Burnley, only to see his close-range shot stopped by Dimitar Evtimov.
But Burton made the most of their reprieve as they levelled after 62 minutes.
A swift counter saw Templeton set free, and though his run broke down, Burnley failed to clear and Liam Boyce’s 20-yard drive flew past Heaton, who should have done better at his near post.
Dyche had seen enough and brought on Ashley Barnes, fresh from his brace against Bournemouth.
And the striker brushed the post with an 18-yard strike just a minute after his arrival, before heading back to Ashley Westwood, who blazed over.
The Clarets were now piling on the pressure and Wood made Evtimov work with a close-range effort.
But it was to be the hosts who had the final say as Boyce slipped in Allen, who fired past Heaton to send the Pirelli Stadium wild.
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