Fernandes, who has 64 goals and 54 assists in 185 games for the club in all competitions, captained in the absence of Maguire, who spent much of last season on the bench or injured.
The defender has been linked in British media reports with a move away from the club.
"The Portuguese midfielder has already worn the armband for United on numerous occasions and Erik ten Hag has confirmed that he will now lead the team on a permanent basis," United said in a statement.
"As captain, the two-time Sir Matt Busby Player of the Year will continue to drive the highest standards throughout the squad as United push for success in the 2023-24 season and beyond."
Fernandes drew criticism for his petulant performance in the 7-0 loss to rivals Liverpool in March.
United's pre-season campaign is underway, with the Old Trafford outfit beating Ligue 1 side Olympique Lyonnais 1-0 on Wednesday.
United will be back in action in next season's Champions League after failing to qualify for the tournament in the 2021-22 campaign.