Fernandes, a £47m January signing from Sporting Lisbon, converted a 42nd-minute penalty after he had been taken out by Watford keeper Ben Foster.
The goal ended a 236-minute wait for a United home goal in the Premier League after they had failed to score against Burnley and Wolves.
Anthony Martial scored an excellent second on Sunday after Watford’s Troy Deeney had a goal ruled out by VAR for handball in the build-up. Mason Greenwood, 18, lashed home his 11th of the season 15 minutes from time to complete United’s scoring.
After beating Chelsea at Stamford Bridge on Monday, it was only the third time this season that United had won successive Premier League games.
While Ole Gunnar Solskjaer’s men have now moved into the top five, Watford remain second from bottom.
Fernandes’ Old Trafford arrival has provided an injection of enthusiasm on and off the pitch.
The United fans sing “Bruno, Bruno” in the way they used to chant Wayne Rooney’s name. They certainly respond to his directness, and it was from one such burst that Foster brought him down for the goal.
Given the midfielder’s elaborate jump as he ran up to take the kick, he needed to score – and he did, with Foster diving the wrong way.
Martial also seems to have responded to Fernandes’ arrival.
The Frenchman’s latest goal means he has found the net in three consecutive games for the first time since September 2017.
The manner of it was superb – first nudging Christian Kabasele aside, then brilliantly finding space with a neat bit of skill after Foster’s initial save had returned the ball to him before keeping his composure to chip into an empty net.
Greenwood has taken a back seat in recent weeks after all the attention he was afforded in the early part of the season, but he also made his mark by smashing a shot into the roof of Watford’s net to end any lingering hopes of a Watford comeback.
Watford’s noisy band of supporters cannot have travelled north with much optimism.
Their side have still never won at Old Trafford, and have now lost nine in a row since their last draw in 1995.
They did have chances. Deeney took too long to try to profit from a ridiculous early mix-up in the home defence, and Luke Shaw snuffed out the chance. Abdoulaye Doucoure also forced a decent save out of David de Gea when the game was still goalless.
There was also the obligatory chant against VAR – in front of watching referee’s chief Mike Riley – after Deeney’s ‘equaliser’ was ruled out, although the handball decision given against defender Craig Dawson as he met the corner that preceded the goal was automatic under the current regulations.
After an encouraging start under Nigel Pearson, who became their third manager of the season on 6 December, Watford have now collected a single point from their last four games.
They still have to play Leicester and Manchester City, who have already beaten them 8-0 this season, in a tricky run-in that begins against Liverpool at Vicarage Road on 29 February.
Harry Gregg remembered
Prior to the game, there was an impeccably observed minute’s silence for former United keeper Harry Gregg, who died on 16 February, aged 87.
In addition to a the silence, a banner was pulled across the Stretford End, proclaiming Gregg’s name with a picture of the man who will forever be remembered for pulling survivors out of the wreckage following the Munich air crash in 1958, in which eight of his team-mates were killed.
Sir Bobby Charlton, who watched today’s game from the directors’ box, is the only player from that day still alive.
Man of the match – Bruno Fernandes (Manchester United)
Manchester United’s next game is on Thursday, when they entertain Club Brugge in the second leg of their Europa League last-32 tie, currently level at 1-1. They then visit Everton next Sunday, 1 March, in the Premier League (14:00 GMT).
Watford’s next game is at home to Premier League leaders Liverpool on Saturday, 29 February (17:30 GMT).