Referee Anthony Taylor pointed straight to the spot for what was the 92nd penalty of this Premier League season, equalling the number awarded in the entirety of the 2019-20 campaign.
Fernandes, no stranger to penalties himself, thumped home his 10th spot-kick of the season despite Ederson getting a hand to his shot.
City were unusually rocky in the opening minutes and they were almost punished again moments later when Joao Cancelo failed to dribble out of his own area. Shaw seized possession but shot straight at Ederson.
Rashford tried his luck from long range but Ederson grabbed his effort at the second attempt.
Ole Gunnar Solskjaer says Anthony Martial looked like he was back to his best in Manchester United's 2-0 win at Manchester City on Sunday, even though the striker was a doubt to feature just hours before the match.
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