The Clarets missed the chance to go third in the table with a game to go as they suffered a second defeat in three games.
And again, Tony Philliskirk’s youngsters let slip a two-goal lead as Queens Park Rangers struck three times after the break to take the points.
The Clarets had fought back themselves earlier on, with Will Harris (pictured above) scoring twice after the visitors had led from the penalty spot in the first half.
Ni-Jai Tucker then increased Burnley’s lead when he made 3-1 five minutes into the second half.
But for the third time in four games, the Clarets were unable to protect a two-goal advantage as the Hoops hit back to claim a late winner through Nathan Carlyle after the dismissal of defender Joel Connolly had left the hosts with 10 men.
In windy conditions at the Barnfield Training Centre, the sides served up a decent game with both enjoying spells in the ascendency.
QPR, also fourth in the southern section of the Professional Development League, went ahead a quarter of an hour in when Dillon De Silva was tripped by makeshift left-back Vinnie Steels and Joseph Gubbins slotted home from the penalty spot.
But two goals in 17 minutes from Harris turned the tide the Clarets’ way.
The striker finished coolly on both occasions, running onto a bouncing ball to steer home the equaliser before capitalising on a fine run from Rhys Fenlon to stroke home his second.
Captain Chris Conn-Clarke, busy pulling the strings from central midfield, had also gone close with a long-range effort as the Clarets played with the wind at their backs.
That was then to benefit the visitors after the break, but not before Burnley had added to their lead through winger Tucker, who drilled the ball home from the left-hand side of the penalty area.
Crucially, Philliskirk’s men couldn’t keep that two-goal cushion for long, though, as a mis-cued pass from Joe Conley invited pressure which ultimately saw substitute Khaliq Raymiond-Callender force the ball home.
Giant striker Hamzad Kargbo then headed just over but with the visitors’ momentum growing, their decision to push Carlyle forward into midfield paid off.
Mitch George saw an effort go into the side-netting from a Tucker cross as the Clarets relieved the pressure.
But with 20 minutes to go Carlyle advanced into the box to side-foot home the equaliser.
And then after full-back Connolly had been dismissed for a second yellow card as he tripped De Silva, the Londoners struck again a minute from time when a ball over the top from the impressive Aaron Drewe found Carlyle to curl home the winner.
The result ended the Clarets’ mathematical chance of a top-two finish and they now need to win at Cardiff on Saturday and hope Nottingham Forest slip up at Crystal Palace in their final game to finish third in the league’s northern group.
Burnley: Allen, Connolly, Steels, Conley, Chima, Pruti, Fenlon (Moonan 85), Conn-Clarke, Harris, George (Major 70), Tucker. Substitutes: Calderbank-Park, McGlynn.
QPR: Little, Drewe, Pitblado, Frailing, Carlyle, Gubbins, Asamoah (Callender HT), Dalipi (Mahorn 65), Kargbo, Mema, De Silva. Substitutes: Middlehurst.