Fernandes tied the league record of 20 assists jointly held by former Arsenal striker Thierry Henry and ex-Manchester City playmaker Kevin De Bruyne.
The Portugal international also scored eight goals as United secured a third-place finish to qualify for the Champions League.
The 31-year-old was nominated alongside Arsenal's title-winning trio of Gabriel, David Raya and Declan Rice, Manchester City duo Erling Haaland and Antoine Semenyo, Nottingham Forest midfielder Morgan Gibbs-White and Brentford striker Igor Thiago.
Fernandes emerged as the Premier League's best playmaker this season when he created a league-high 132 chances. The next best player was Liverpool's Dominik Szoboszlai, who created 89 chances.
Fernandes was named the Football Writers' Association men's player of the year earlier this month, while he also picked up the club's Sir Matt Busby Player of the Year honour for the fifth time.
He has the opportunity to make the Premier League assists record his own on Sunday when United travel to Brighton & Hove Albion for the final game of the season.
O'Reilly named best young player
Manchester City's Nico O'Reilly was named the Premier League Young Player of the Season after the 21-year-old had a breakthrough campaign which has earned him a spot in England's World Cup squad.
O'Reilly, who came through City's academy, broke into Pep Guardiola's starting line-up this season, predominantly playing as a left back while also making appearances in midfield, scoring five goals and providing three assists in the league.
He has made 34 league appearances this season, with 29 starts, while he has scored crucial goals in big games, including a brace in City's 2-0 win over Arsenal in the League Cup final.
"I'm very proud to have won this award. After my first appearances in senior football last season, I knew this year I could have the opportunity to play more and help the team as much as possible if I worked hard," he said.
"To get so many minutes and earn the trust of the manager and my teammates has been the greatest achievement in my career so far. I am so grateful to my family and everyone at City because this wouldn't have been possible without them."