Ole Gunnar Solskjaer’s side got off to the worst possible start when the ball deflected off Luke Shaw for an own goal in the second minute, but United captain Harry Maguire put his side level from a corner in the 23rd minute.
Goalkeepers Karl Darlow and David de Gea were in top form.
Spaniard de Gea pulled off a brilliant reflex save to deny Allan Saint-Maximin, while Darlow also made a string of fine saves at the other end.
The visitors should have gone ahead from the spot after Marcus Rashford was fouled, but again Darlow was up to the task, beating the spot kick from Fernandes away with his forearm.
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However, the Newcastle goalkeeper appeared to be troubled by an injury to his left groin and Fernandes made no mistake four minutes from time, finishing off a superb flowing counter attack by lashing the ball into the top right corner to give his side the lead.
Newcastle crumbled in the final minutes as Aaron Wan-Bissaka stepped up to fire into the same top corner for his first senior goal in stoppage time, and Rashford added a fourth with a cleverly-timed run and cool finish to complete the rout.
The win puts Manchester United 14th on six points, while Newcastle are 11th on seven points.