United crashed out of the FA Cup on Sunday afternoon in a 3-1 defeat to the Foxes and it was a heavily rotated side.
One of the biggest names missing out however was Fernandes, who didn't come on until the second half.
Manager Ole Gunnar Solskjaer explained the decision post-match and said it was for 'the benefit of the team.'
He stated per Daily Mirror: "Every team selection has reasons behind it and Bruno has played a lot of football, on Thursday night he broke all his records physically, statistically and the boy is not inhuman.
"He has played a game every three or four days and it was a chance to start both Donny [van de Beek and Paul [Pogba], but the accumulation of games maybe caught up with us.
"Bruno wants to play and sometimes you make decisions for the benefit of the team."
Fernandes played the full 90 minutes at the San Siro on Thursday as United ran out 1-0 winners in the Europa League.
Donny van de Beek, Nemanja Matic and Fred started the game in midfield, but all three would end up replaced throughout the game.
Neither of the trio had particularly strong games and Fred even made a mistake to allow Kelechi Iheanacho to open the scoring.
When asked if he'd make the same team selection again given the chance, Solskjaer replied: "I would've done the same again, the changes were necessary to do.
"We knew Paul [Pogba] wouldn't last more than an hour and I don't think I would do anything differently. What goes on behind the scenes isn't always known.
"I would have started the same team again.
"We felt they had more than 45 minutes in them, they're important players for us, that's why we started [with them]."
Iheanacho scored either side of Youri Tielemans' low drive to give Leicester a legendary win
They'll face Southampton in the semi-finals for a chance to face either Manchester City or Chelsea in the final.
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