The Red Devils clawed their way back into the clash against their rivals from 12 yards after Matheus Nunes clumsily fouled Amad Diallo in the 86th minute.
Diallo would go on to score his side's winner in stoppage time, and the result meant that head coach Ruben Amorim has now won as many games - four victories in seven — as previous boss Erik ten Hag managed in 14 games this term.
Captain Fernandes also reached a significant milestone in his United career given his strike was the 21st penalty he has scored for the Red Devils in the Premier League, surpassing Wayne Rooney's record of 20 to become the outright leader in terms of goals from spot kicks for United in the competition's history.
It should come as no surprise that the Portuguese found the back of the net considering he has remarkably converted 56 of his 62 penalties in his career, including 21 of his 25 penalties in the English top flight.
Fernandes's vital role
Fernandes has long been a favourite of United fans, and he has already seemingly become a favourite of Amorim, who has started the 30-year-old in all seven of his games in charge.
There is no doubt that the midfielder can become a key part of Amorim's team over the next few years, with the midfielder's immense creativity making him a natural fit in the manager's 3-4-3 system.
Fernandes has created the most chances and the most big chances, while his tally of nine goals and assists is the most of any player at the club.
In addition to his immense output, he also works incredibly hard without the ball and can never be accused of not giving his all, even if his performances have not always been of the highest standard.
If United are to succeed under Amorim in the short to medium term, then they will need to rely on Fernandes's composure, workrate and productivity.
Is his age a problem?
While the midfielder has arguably been United's best signing in the post-Alex Ferguson era, he is no longer a youngster and it remains to be seen if he can continue to be so influential.
Though many players have been effective once they are in their thirties, it could be some time before Amorim is able to build a United squad capable of challenging for the Premier League title.
Fernandes is almost certain to be a key figure under the new boss in the immediate future, but it is plausible that he could decline before Amorim's United reach their potential.
The Red Devils are currently 13th in the Premier League with 22 points after 16 outings, though the six-point gap to fourth-placed Nottingham Forest is by no means irrecoverable.
Man United will have to prove that they can overcome some of the issues that have plagued the club if they are to make a push for the division's four Champions League spots, and Fernandes will no doubt be central to club's fortunes this season.
Written by
Lewis Nolan