Ole Gunnar Solskjaer’s side rode their luck on the south coast, as Brighton hit the woodwork five times, but fortune was on their side as Fernandes sealed a dramatic three points.
The Seagulls bossed the first half right from kick off, as Leandro Trossard cracked an early effort off the post.
But the hosts coming in waves is was only a matter of time before Graham Potter’s side found a breakthrough, with Neil Maupay edging them in front on 40 minutes.
Fernandes bundled over man of the moment Tariq Lamptey inside the box, and the Frenchman dinked home from the spot.
Despite failing to make any inroads, United levelled things up just before the break, as Lewis Dunk diverted Harry Maguire’s flick into his own net.
That slice of luck tipped the game in United’s favour as Marcus Rashford fired them in front after the restart.
The England star was quiet in the first half, but he showed a burst of pace to get away from Ben White, before rocketing past Matt Ryan.
But Brighton were not about to roll over in the second half, as Solly March tested the post and David De Gea produced a fine stop from Maupay.
However, as the game ticked into added time, there was drama at both ends.
March thought he had secured a late point for Brighton with a brave header, but after a whopping ten minutes of added time, penalty king Fernandes fired home the winner.
FULL TIME AT THE END OF A MENTAL AFTERNOON AT THE AMEX STADIUM IT’S BRIGHTON 2 MANCHESTER UNITED 3