The Clarets’ bid to reach the semi-finals of the Premier League Cup was ended by two second-half goals as Leeds kept their double hopes alive.
Having already won the northern section of the U23 Professional Development League – with Burnley still hoping to join them in the national play-offs – Leeds advanced into the last four of the competition.
But the Yorkshiremen were given a major scare at the Barnfield Training Centre as the Clarets threatened a successful comeback to keep their own cup run going.
Dan Agyei, whose winning goals had seen off West Bromwich Albion and Leicester City to take Steve Stone’s side into the last eight, equalised just before the break.
And the Clarets then dominated the early stages of the second half with substitute Josh Benson missing a chance to mark his comeback from injury with a goal to put Burnley in front.
Defender Bobby Thomas had also hit the top of the bar with a header and might have had a penalty when he was pulled down in the box.
But Leeds restored their lead when Ryan Edmondson headed home and a third goal nine minutes from the end finally ended the Clarets’ hopes.
Having lost in the league at Bristol City on Monday, Burnley were looking to respond and were inches away from taking an early lead as they bounced back to form with an impressive performance.
Jordan Cropper’s fierce long-range effort was top-corner bound until Leeds keeper Harrison Male touched the ball onto the bar at full stretch.
And Leeds went ahead from virtually their first foray forward, Christian N’Guessan powerless to keep the ball out of the net after Aapo Halme’s flicked effort from a corner had come back off the far post and bounced in off the Clarets' midfielder with 15 minutes gone.
Winger Tunde Bayode led the fightback as he got the Clarets on the front foot with a free-kick turned around the post by Male.
And Burnley’s growing pressure paid off just before the break as Tinashe Chakwana did well to deliver from the left and top scorer Agyei fired home on the turn after N’Guessan had forced the ball goalwards.
The momentum stayed with the Clarets after the break as they camped in the Leeds’ half for the first 15 minutes.
But the second goal wouldn’t come as Thomas and Benson both went close before the Clarets paid the price for a dis-jointed five minutes as Clarke Oduor crossed for Edmondson to head powerfully home.
Chakwana thought he had equalised for a second time but his effort was ruled out for a foul by Thomas.
And with time running out, any chance of a comeback was snuffed out when Hugo Diaz headed in from a free-kick to end a cup run for the Clarets which started with a 7-1 defeat at Bournemouth but then carried them unbeaten through six games of a superb season-long campaign that didn't end without a fight.
Burnley: Legzdins, Cropper, Thomas, Wilson, Glennon; Bayode (Blair 56), Howarth (Benson 50), N’Guessan, Chakwana; Agyei, Richardson (Harris 66). Substitutes: Stone, Clarke.
Leeds United: Male, Hosannah, Davis, Diaz, Halme (Mihaylov HT), Struijk, Stevens, Gotts (Casey 90), Edmondson, Bogusz (McCalmont 88). Substitutes: Rae, Nicell.
Referee: Simon Mather