Mason Greenwood’s sixth league goal of the season gave United the lead inside 16 minutes at the Amex Stadium before Fernandes combined with Paul Pogba to double their tally before the half-hour mark.
Fernandes then extinguished Brighton’s second-half revival as his emphatic volley rounded off a devastating United counter within five minutes of the restart.
David de Gea prevented Aaron Connolly, Neal Maupay and the lively Leandro Trossard from registering a deserved Brighton consolation after an improved second-half display, but the damage was done as they tasted their first defeat since the restart.
The victory extends United’s unbeaten run to 15 games and lifts them up to fifth, two points behind fourth-placed Chelsea ahead of their trip to West Ham on Wednesday. Brighton stay 15th, six clear of the relegation zone.
Brighton travel to Norwich on Saturday at 12.30pm, before Manchester United host Bournemouth on Saturday at 3pm.