Sam Johnstone, playing against the team he joined as a 10-year-old, made two outstanding saves in the first half to deny Anthony Martial.
But this game will be remembered for a crazy spell shortly after the re-start that meant it was VAR - and referee David Coote - who came away the main talking points.
In the 53rd minute, Coote awarded Albion a penalty after Fernandes fouled Conor Gallagher in the box.
The Portugese midfielder did get a touch on the ball but then took the man in what looked a clear spot-kick.
But Coote, after being called to his monitor, decided to overturn his decision despite it appearing that - anywhere else on the pitch - it would have been a foul.
To add insult to injury, United were then awarded a penalty of their own when Juan Mata’s cross hit the arm of Darnell Furlong with his back turned.
Fernandes took it and saw his effort saved by Johnstone. But VAR judged the keeper had strayed from his line and ordered it to be retaken. And at the second attempt, Fernandes did score.
Incredibly Albion then saw substitute Callum Robinson rattle the crossbar with a fierce effort from 20-yards.
But despite a display full of grit, guts and determination, they couldn’t find an equaliser and that meant they were forced to come away with nothing.
In his pre-match press conference, boss Slaven Bilic confirmed “one or two” of his players would miss the trip to Old Trafford after contracting COVID-19.
And he confirmed just before kick-off those men were skipper Jake Livermore and Kieran Gibbs who both had to join fans watching at home.
The boss also revealed he was forced to name some players on the bench - who otherwise would have started - after they had been unable to train for 10 days having previously tested positive for coronavirus.
While his preparations had been severely disrupted by the virus, Bilic was able to stick with the 5-3-2 formation that worked well against Tottenham - albeit with some small tweaks.
In the midfield three, Matheus Pereira, having recovered from COVID-19, joined forces with Romaine Sawyers and Conor Gallagher.
Grady Diangana then joined Karlan Grant up front.
Manchester United lined up in a 4-2-3-1 system with Anthony Martial the central striker.
Bruno Fernandes operated just behind him in the number 10 role with Marcus Rashford on the left and Juan Mata on the right.
In what was a captivating opening 20 minutes, the hosts created two big chances to open the scoring.
The first arrived from a set-piece with Martial meeting a Fernandes delivery with a clever header.
Johnstone kept it out with an impressive one-handed stop. But if that save was good, the keeper’s next was spectacular.
After a Semi Ajayi pass was intercepted, Solskjaer’s men broke at pace with Rashford finding Fernandes in the box who then squared for Martial.
Just eight-yards-out, the Frenchman looked destined to open the scoring but Johnstone got down brilliantly and produced a strong arm to parry the ball away.
Those two chances aside, Albion had acquitted themselves well as the half reached the midway point with Bilic’s side disciplined and organised in a relatively new system.
The key was making the most of the opportunities that did come their way.
And they came close to opening the scoring when Pereira brilliantly slipped the ball through the legs of Nemanja Matic before sending Grant charging towards goal.
From just outside the box, the striker then arrowed a smart low drive that, at full-stretch, David de Gea tipped around the post.
From the resultant corner, Branislav Ivanovic headed over.
While United were enjoying a lot of the ball, they were struggling to break through Albion’s resolute defence.
And Bilic’s men had an another opportunity to get their noses in front just before the break when Kyle Bartley met a corner only to see his deft header sail over.
It meant the two teams made their way off at the break with United having enjoyed 66 per cent possession but with Albion having stuck to their game plan impeccably.
While the first half had been fascinating to watch the game would ultimately be remembered for what happened inside the opening stages after the re-start - with VAR well and truly taking centre-stage.
The madness started in the 53rd minute when Albion were awarded a penalty after Gallagher was tripped by Fernandes in the box.
The Portugese midfielder did get a touch on the ball but then took out the man for what looked a clear spot-kick.
But referee David Coote was called to look at his monitor.
And he then decided to change his mind despite the fact Fernandes foul would have been a free-kick anywhere else on the pitch.
If that wasn’t bad enough, United were then given a penalty of their own when Fernandes sent in a cross which hit the arm of Furlong with his back turned.
It was a handball that, in previous years, wouldn’t have been a spot-kick and it felt as though justice had been done when Johnstone made a brilliant save to deny Fernandes from 12-yards.
But referee Coote again headed to VAR and judged that Albion’s keeper had come off his goal-line.
And that meant the penalty was re-taken with Fernandes scoring at the second attempt.
It was an incredible turn of events.
And you couldn’t help but feel the gods were against Albion when substitute Hal Robson-Kanu did really well to hold-up the ball and send Gallagher away.
He then found fellow sub Callum Robinson who hit a fierce effort from 20-yards which beat de Gea but cannoned against the crossbar.
With Albion pushing forward, United became more dangerous with Johnstone making two other excellent stops to deny Rashford and Harry Maguire.
Man United: De Gea, Wan-Bissaka, Maguire, Lindelof, Telles, Fred (McTominay 83), Matic, Fernandes, Mata (Cavani 67), Rashford (Van de Beek 79), Martial.
Subs not used: Henderson, Willians, Van de Beek, Tuanzebe, McTominay, James, Cavani
Albion: Johnstone, Furlong, Bartley, Ajayi, Ivanovic (Krovinovic 79), Townsend, Sawyers, Gallagher, Pereira, Diangana (Robson-Kanu 62), Grant (Robinson 62).
Subs not used: Button, O'Shea, Harper, Phillips.