The Clarets looked to continuing their positive start to the season by claiming a 2-2 draw at Old Trafford, after fighting back not once, not twice to level.
But referee Sam Barrott overturned a late decision not to award United a penalty, with Bruno Fernandes stepping up and slotting home to win it for the home side at the death.
VAR had earlier got involved to deny Lyle Foster a second goal when he rounded the keeper to slot home, only to be ruled offside by the barest of margins.
United also had a first-half penalty overturned after Kyle Walker and Mason Mount had tussled right on the 18-yard box.
Here’s how Burnley’s players rated:
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1. Martin Dubravka - 8/10
Made a string of fine stops during the first-half to keep the scores down to one, otherwise Burnley would have been out of the game. (Photo by OLI SCARFF/AFP via Getty Images) Photo: OLI SCARFF
2. Kyle Walker - 6/10
Right decision not to award the penalty, but Walker still didn’t need to be so rash. Harshly penalised for the free-kick that led to United’s opener. Long throws caused problems. (Photo by OLI SCARFF/AFP via Getty Images) Photo: OLI SCARFF
3. Hjalmar Ekdal - 7/10
Won so many headers late on as United loaded the box in search of a winner. On the front foot and used his physicality well. (Photo by Jan Kruger/Getty Images) Photo: Jan Kruger
4. Maxime Esteve - 7/10
Provided the flick-on for Burnley’s second goal, which caused havoc in the United box. Stood up well to United’s attacking pressure. (Photo by Jan Kruger/Getty Images) Photo: Jan Kruger