The 31-year-old delivered a decisive season, scoring eight goals and equalling the record for most assists in a single Premier League campaign with 20, matching the benchmarks set by Thierry Henry and Kevin De Bruyne.
His consistency and leadership were key factors in United's push to secure Champions League qualification, with Fernandes now becoming the first United player to win the award since Nemanja Matic in the 2010/11 season.
He also joins an elite group of United winners, alongside legends such as Peter Schmeichel, Dwight Yorke, Ruud van Nistelrooy, Cristiano Ronaldo and Wayne Rooney.
Fernandes beat strong competition for the award, including Arsenal trio David Raya, Gabriel Magalhães and Declan Rice.
Also among the nominees were Manchester City striker Erling Haaland, who is closing in on a third consecutive Golden Boot with 27 goals, along with Antoine Semenyo, Morgan Gibbs-White and Brentford striker Igor Thiago.
The award caps a major individual season for Fernandes, who once again proved central to United's attacking rhythm and overall success in the Premier League campaign.