Fernandes put Man Utd ahead on 42 minutes, slotting past Ben Foster from the penalty spot after he was brought down by the Watford goalkeeper.
Watford's Troy Deeney then had a goal overturned by the Video Assistant Referee after Craig Dawson was adjudged to have handled in the build-up.
Anthony Martial doubled Man Utd's lead in the 58th minute in sublime style, skilfully beating a defender before chipping the ball over Foster.
It was 3-0 with 15 minutes remaining when Fernandes fed Mason Greenwood, who smashed the ball in off the underside of the crossbar.
Back-to-back victories leave United three points behind fourth-placed Chelsea.
Watford remain 19th with 24 points, one adrift of Aston Villa in 17th.
Man Utd: 1 Mar v Everton (A)
Watford: 29 Feb v Liverpool (H)