The visitors had an early Scott McTominay goal controversially disallowed for an offside on Harry Maguire, and it did appear that the points would be shared in the English capital.
However, Fernandes came up with the winner in the final exchanges to secure a huge three points for Erik ten Hag’s side, who have moved into sixth position in the Premier League table on 18 points.
Maguire went down inside the first minute, with the centre-back taking a heavy blow to his face in a challenge with Fulham’s Rodrigo Muniz, but he was able to return to the field after a period of recovery.
Man United thought that they had made the breakthrough in the eighth minute, with McTominay turning into the back of the net from close range after Alejandro Garnacho had delivered a brilliant cross into the penalty box.
However, the goal was disallowed, following a four-minute VAR review, for an offside on Maguire, who made an attempt to play the ball and was therefore deemed active, with the decision controversial at best due to the lack of consistency in similar situations this season.
Fulham’s first shot came from Harry Wilson, drawing a smart save from Andre Onana, although the offside flag had been raised slightly before the powerful effort.
Aaron Wan-Bissaka did well to deflect a Willian effort wide of the post in the 23rd minute, before Wilson struck one over the crossbar from the resulting corner, with both sides having their moments in the final third.
Brilliant defending from Diogo Dalot, who was in at left-back, prevented Wilson from potentially having a tap-in in the 28th minute during a strong period for Fulham.
Jonny Evans sent an acrobatic effort wide of the post in the 32nd minute, before Fulham goalkeeper Bernd Leno kept out a strike from Bruno Fernandes shortly after.
Alex Iwobi smashed one wide of the Man United goal on the counter-attack in the 38th minute after the Red Devils had again conceded possession in a dangerous area, before Dalot hit one over the crossbar down the other end, with the two sides level at 0-0 approaching the break.
Willian had the final chance of the half, dropping his shoulder before curling one wide of the far post, with Fulham finishing the opening 45 minutes on the front foot.
Garnacho brought a smart save from Leno early in the second period, before the same two players locked horns in the 51st minute, with the Fulham goalkeeper again coming out on top.
Another counter-attack brought a chance for Fulham in the 57th minute, but there were no takers on Willian’s low cross into the box, with Maguire doing well to deal with the danger.
Maguire then made another big block on a shot from Willian, before the Fulham attacker whipped one just wide of the near post, with the home side threatening to make the breakthrough.
Onana kept out a powerful strike from Wilson in the 61st minute before McTominay managed to clear ahead of Pereira from the rebound, and the Man United goalkeeper then made a brilliant stop to deny Joao Palhinha.
Dalot cleared an effort from Calvin Bassey off the line from the resulting corner, before Muniz headed a corner just over the crossbar, with Fulham really threatening to make the breakthrough.
Facundo Pellistri, who replaced the disappointing Antony, saw a low strike kept out by Leno in the 71st minute, before Iwobi fired one over the target down the other end, with the score remaining level heading towards the final 15 minutes of action in the English capital.
Dalot whistled one wide of the post in the 79th minute, before Mason Mount and Anthony Martial were introduced for Man United for the final 10 minutes.
Leno did well to keep out a Fernandes free kick in the 83rd minute, before Martial turned a cross from Dalot wide of the post in the 84th minute with an acrobatic effort.
Ten Hag’s side won it in the final moments, though, with the Portugal international creating space on the edge of the box before finding a route into the bottom corner to spark jubilant scenes in the away end.
Man United will now travel to Denmark for a key Champions League fixture with Copenhagen, while Fulham are back in league action away to an in-form Aston Villa next weekend.
