Martial's strike at the Jan Breydel Stadium spared Ole Gunnar Solskjaer's blushes and ensured that United's unbeaten run remained intact.
Fernandes netted one and played a part in the other two goals - scored by Martial and Mason Greenwood - as United moved into fifth place, which would like be enough for a Champions League qualification spot.
United have finally hit a purple patch of sorts, but it is somewhat worrying that they have not won back-to-back matches since the end of last year.
A goalless draw would still be enough for the Red Devils on Thursday given Martial's away goal, but Solskjaer will not want to do things the hard way.
This is a competition United won two seasons ago and they are unbeaten in their last 12 home Europa League games since losing to Marcelo Bielsa's Athletic Bilbao in March 2012.
Worryingly for Brugge, who are now unbeaten in 14 matches since before Christmas after beating Charleroi on Sunday, they have never won an away European match in England.
That run includes two draws and 10 defeats, most recently losing 2-1 to Leicester City in a Champions League match three seasons ago.
However, Philippe Clement's men have already picked up a 2-2 draw at Real Madrid in the Champions League this term - albeit after throwing away a two-goal lead - and the first leg showed they should not be entirely written off.
Manchester United's Europa League form: DWWLWD
Manchester United's form (all competitions): WWDWDW
Club Brugge's Europa League form: D
Club Brugge's form (all competitions): WWDWDW
The Scotland international played 11 minutes from the bench and, given his importance in the weeks leading up to his injury, he could be thrown back into the starting XI here.
Brandon Williams, Sergio Romero and Eric Bailly are all pushing for recalls after missing out against Watford, while Juan Mata and Jesse Lingard are also looking to force their way back into the side - and indeed into the squad in the case of the latter.
Elsewhere, Odion Ighalo has made three substitute appearances since joining last month and could be in line for a full debut on Thursday.
As for the visitors, they have been dealt a huge double injury blow ahead of the match.
Dennis, their goalscorer in the first leg, has not been included in their squad and club captain Ruud Vormer is also absent after both men picked up injuries against Charleroi.
Defensive midfielder Eder Balanta is also missing due to suspension.
Manchester United possible starting lineup:
Romero; Wan-Bissaka, Bailly, Maguire, Williams; Pereira, McTominay; Greenwood, Fernandes, James; Martial
Club Brugge possible starting lineup:
Mignolet; Mata, Mechele, Deli; Kossounou, Sobol, Rits, Cuyper; Tau; Openda, Vanaken
We say: Manchester United 2-0 Club Brugge (3-1 on aggregate)
United have left themselves with work to do following last week's draw in Belgium, but Solskjaer is expected to name a fairly strong lineup and the Red Devils should have enough to get the job done at Old Trafford.