Fernandes set up Patrick Dorgu's 33rd-minute header from a corner — his 21st assist of the season — moving him clear of Thierry Henry and Kevin De Bruyne, who had jointly held the record since 2002-03 and 2019-20 respectively.
He then scored United's third shortly after half-time to finish the campaign with nine goals and 21 assists in 38 league appearances.
Bryan Mbeumo added United's second goal in between Fernandes' contributions, as Michael Carrick's side ended the season at Brighton with their 12th win from 17 matches under the new permanent manager.
Carrick was asked about the prospect of Fernandes, whose contract runs until June 2027 with an option to extend by a further year, being tempted away again after coming close to joining Saudi Arabia's Al-Hilal last summer. His answer was unequivocal.
"He loves being here. I think you can see that. He wanted to stay on, he wants to stay on every single game because he's enjoying his football. We've loved what he's done. I've got no reason to think otherwise."
Fernandes, who was named the Premier League's player of the season and the Football Writers' Association men's player of the year earlier in the week, spoke about the confirmation of Carrick's appointment.
"Obviously it's a very important step for our club. We need stability in terms of managing. Since Michael came to the club, you know the calmness he gives to the team. He knows the club, what it means and what it demands to be at this club. We are very excited for what is coming."
Manchester United finish third in the Premier League, returning to the Champions League for the first time since the 2023-24 season.