Ole Gunnar Solskjaer's side suffered a humiliating 6-1 defeat against Tottenham at Old Trafford just before the international break.
But they made partial amends for that embarrassment with a much-needed second win of the Premier League season.
After Luke Shaw's own goal gave Newcastle an early lead, United captain Maguire scored the equaliser just days after he was widely criticised for his red card in England's Nations League defeat against Denmark at Wembley.
Maguire's first Premier League goal since February was a cathartic moment after a troubled few months marred by poor performance on the pitch and his Greek court case off it.
Fernandes also went from zero to hero as the midfielder's second half penalty was saved by Karl Darlow, before he hit a superb strike to put United ahead in the closing minutes.
Aaron Wan-Bissaka made it three with his first goal for United and Marcus Rashford wrapped up the late goal blitz in stoppage-time.
Although United left it late to finish off Newcastle, the result was no more than they deserved and Solskjaer will hope it is the start of a better period for his team after their troubled opening to the campaign.
After labelling the Tottenham rout as the "worst" day of his career, Solskjaer made five changes for United's return to action.
Eric Bailly, Nemanja Matic, Paul Pogba, Mason Greenwood and Anthony Martial were replaced by Victor Lindelof, Scott McTominay, Fred, Daniel James and Juan Mata.
Moment to savour
Solskjaer's switches initially did nothing to improve United's fortunes as Newcastle cut through them in the second minute.
Allain Saint-Maximin and Jonjo Shelvey combined to find Emil Krafth on the right side of the United penalty area and his cross took a deflection off Shaw's out-stretched leg as it looped beyond David De Gea.
United thought they had equalised in the 19th minute when Fernandes fired into the top corner from Mata's pass, but VAR intervened to rule that the Spanish midfielder was offside before he provided the assist.
If Solskjaer feared it was going to be another dispiriting night, his concerns were eased as Maguire finally enjoyed a moment to savour in the 23rd minute.
Timing his run to meet Mata's corner, Maguire got in front of Jamal Lascelles at the near post and guided his header past Darlow from six yards.
Saint-Maximin nearly restored Newcastle's lead with a powerful shot that De Gea turned away while clattering into a post, leaving United's keeper needing treatment on his shoulder before he could continue.
Wan-Bissaka brought a superb save from Darlow before Rashford's shot was cleared off the line by Lascelles from the resulting corner.
De Gea made an alert save to prevent Callum Wilson's close-range effort from Saint-Maximin's cross putting Newcastle ahead soon after the break.
When Rashford was brought down by Jamal Lewis in the 57th minute, referee Craig Pawson initially appeared to ignore the offence but after consulting the pitchside monitor he ruled that the foul had taken place inside the penalty area.
Fernandes has been a penalty expert for United since arriving in January, but for once he fluffed his lines as Darlow dived to his right to keep out the midfielder's spot-kick.
Maguire nearly made up for Fernandes' miss when his header was cleared off the line by Shelvey, whose 30-yard blast drew a fine save from De Gea moments later.
But Fernandes had the last laugh anyway as he took Rashford's clever reverse pass in the 86th minute and, from an acute angle, curled an exquisite shot into the top corner.
Wan-Bissaka netted in the 90th minute from Rashford's pass and the provider turned scorer moments later with a cool finish from Fernandes' long ball.