The Reds initially led through goals from Harry Maguire and Fernandes himself but were pegged back early in the second half by the hosts, with Rodrigo and Raphinha scoring within a minute of one another.
But United rallied once more, and late goals from substitutes Fred and Anthony Elanga ensured that Ralf Rangnick’s side took all three points back to Manchester.
Fernandes, who also assisted Elanga's goal, said: “We [kept] on doing the right things, making the right decisions.
“You have to keep doing the right things and taking the right decisions, even if you go down.