The opening game in Group H of the Champions League pits Ole Gunnar Solskjaer's side against last season's beaten finalists in the competition.
Maguire overcame a slight injury to play and score in the 4-1 win over Newcastle United on Saturday night, but he has now been ruled out of the trip to France.
During a press conference in Paris on Monday, Solskjaer confirmed Fernandes will captain United in Maguire's absence.
It marks swift affirmation of the Portugal international's leadership qualities, considering he only joined the club in January and won the Sir Matt Busby Player of the Year award.