Arsene Wenger's final match at Old Trafford as Arsenal manager ended in defeat with a stoppage time header from substitute Marouane Fellaini earning the points for second-placed Manchester United.
Paul Pogba drove United into the lead in the 16th minute, pouncing after Alexis Sanchez had headed a Romelu Lukaku cross against the post.
Arsenal, fielding a largely second string side, drew level in the 51st minute when Henrikh Mkhitaryan, signed from United in January, beat David De Gea with a well-placed effort.
United's Marcus Rashford had the ball in the net in the final minute but the effort was ruled out for offside before Fellaini headed in the stoppage time winner from an Ashley Young cross.
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