The Norwegian’s position at Old Trafford has come under real pressure in recent weeks, but a first half brace from Fernandes set them on the way to three important points.
Both sides looked right up for this high-stakes clash on Merseyside as Dominic Calvert-Lewin headed an early chance wide and man of the moment Marcus Rashford tested the returning Jordan Pickford.
And with the Toffees just about edging it early on, Brazilian winger Bernard found a breakthrough.
Pickford’s long punt forward was flicked on Calvert-Lewin and the former Shakhtar man drilled past David De Gea on 20 minutes.
But despite squeezing themselves in front, Everton’s poor defending was to United allow back into it just five minutes later.
Luke Shaw’s floated cross dropped in between Michael Keane and Mason Holgate and Fernandes arrived on cue to nod past Pickford.
Fernandes then took control of the game for United, testing Pickford with a fine free kick, before grabbing his second of the game before the break.
Rashford clipped a delightful ball into the box and once again Fernandes ghosted in unmarked to head home.
Everton struggled to force their way back into it after the break, and Pickford almost gifted United a goa as he slipped a corner, but Harry Maguire skewed his effort over.
The game did begin to see saw in the closing stages as Pickford denied Rashford and Maguire headed Alex Iwobi’s cross off the line.
Everton almost mustered up an equaliser in added time as Abdoulaye Doucoure miscued Seamus Coleman’s pass wide, but Fernandes was to have the final say with seconds left.
The Portuguese international led a United counter attack in the closing seconds and he laid it on a plate for substitute Edinson Cavani to tuck home his first United goal.
Full Time at Goodison Park it’s Everton 1 Manchester United 3