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A point would have taken United top of the Premier League, with Chelsea losing to Manchester City on Saturday, but it could have no complaints about the outcome at Old Trafford despite a dramatic finish.
Kortney Hause looked to have gone from hero to zero when he followed a headed goal at one end with a handball at the other.
But Fernandes, taking the spot-kick ahead of Cristiano Ronaldo, blazed over the crossbar to condemn United – which lost Harry Maguire and Luke Shaw to injury – to a first league defeat of the campaign.