Fernandes, a £47m January signing from Sporting Lisbon, transformed a 42nd-minute penalty after he had been taken out with the aid of 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 tremendous 2nd after Troy Deeney had a goal ruled out by way of VAR for handball in the build-up, with 18-year-old Mason Greenwood lashing home his eleventh of the season 15 minutes from time.
After beating Chelsea at Stamford Bridge on Monday, it was once solely 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.