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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9. Hannibal - 6/10
Could have levelled against his former side when he lashed over on the turn just 10 yards out. Ran himself into the ground again. (Photo by Matt McNulty/Getty Images) Photo: Matt McNulty
10. Jaidon Anthony - 7/10
Got Burnley back level for a second time as he forced the ball home from close range for his second goal of the season. But ended on a sour note with his shirt pull for the penalty (Photo by OLI SCARFF/AFP via Getty Images) Photo: OLI SCARFF
11. Lyle Foster - 8/10
Got Burnley back level, steering home Bruun Larsen’s pinpoint cross from close range. So unfortunate to have another goal ruled out. (Photo by OLI SCARFF/AFP via Getty Images) Photo: OLI SCARFF
12. SUB: Loum Tchaouna - 6/10
For Hannibal, 65 Almost had an instant off the bench, as it was his shot that was saved for Burnley's second. (Photo by Julian Finney/Getty Images) Photo: Julian Finney