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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13. SUB: Josh Laurent - 7/10
For Ugochukwu, 75 Provided some much-needed energy off the bench to press from the front. Got behind on one occasion but couldn't quite pick out the pass. (Photo by Lewis Storey/Getty Images) Photo: Lewis Storey
14. SUB: Joe Worrall - 6/10
For Ekdal, 82 Brought on towards the death as United loaded the box and threw more and more men forward. Won some important headers. (Photo by Alex Livesey/Getty Images) Photo: Alex Livesey
15. SUB: Oliver Sonne - 6/10
For Bruun Larsen, 82 Didn't play long enough to make an impact either way, but Burnley certainly needed some fresh legs on the pitch towards the death. (Photo by Matt McNulty/Getty Images) Photo: Matt McNulty