The Red Devils were embarrassed at Vicarage Road, with Josh King, Ismalia Sarr, Joao Pedro and Emmanuel Dennis sealing a 4-1 win for the relegation-threatened Hornets.
They have now won just one of their last seven top-flight games, a run of form that has seen them drop to seventh in the table, 12 points behind leaders Chelsea.
The club’s travelling support made their anger towards Solskjaer’s underperforming team clear following the defeat to Claudio Ranieri’s side.
The Norwegian and his United side walked over to the away end to applaud their fans following a fruitless trip down from Manchester.
But as the cameras zoomed in on Solskjaer and his key players, a chorus of boos rained down from their own fans.
That prompted Fernandes to angrily wag his finger at the United supporters before pointing to his team-mates to signal their frustrations should be directed at the players, not the manager.
The visibly anger midfielder was then led away by Fred, an unused substitute, and Solskjaer as they walked back towards the tunnel.
Despite Fernandes’ reaction, Solskjaer took the side of United’s supporters, insisting they had every right to make their anger clear.
“I understand fans who follow the club through thick and thin,” Solskjaer said following the humiliating defeat.
“They’ve been fantastic the last few years, it’s a difficult period, we’ve had a hard time since Sir Alex left and fans who’ve been with us have been unbelievable, understood the situation.
“The signings this summer with Rapha, Jadon and Cristiano have raised expectations, being second we hoped to kick on and at the minute we can’t seem to find our form.
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“I understand, that’s their right to show their opinion. Bruno is such a passionate boy and a man and he knows football can change quickly.”
Solskjaer was unhappy with his side’s dismal performance at Vicarage Road, one that looks set to see him sacked.
“Watford away from home, you need to give them a harder time than we did. They outfought us, we allowed them to put ball in our box too easily,” he acknowledged.
“[For the] first goal, Ben Foster was on the halfway line when he puts that ball in. There are so many things can go wrong in football and too many did in the first half.”
United’s hierarchy are thought to have held an emergency meeting on Saturday night to decide Solskjaer’s future.
But the sacking of the Norwegian now appears to be a formality, with little prospect that he can turn United’s awful form around.
A decision will need to be made quickly though, with the Red Devils set to travel to Villarreal in the Champions League on Tuesday night.