With the game petering out to a goalless draw, Kortney Hause headed home in the 88th minute to seal the victory for the visitors.
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United were given the chance to equalise in stoppage time when referee Mike Dean pointed to the spot after Edinson Cavani‘s header was adjudged to have struck Hause’s arm, but Fernandes hit his effort way over.
Cristiano Ronaldo was back in the starting lineup, having been among the first-team players left out of the Carabao Cup third round defeat to West Ham United, but failed to find the net for the first match since his return.