Striker Jordan Ayew had a penalty saved by Manchester United goalkeeper David De Gea but his blushes were spared after VAR ordered a replay.
The Ghana international won the spot kick after striking the ball against the arm of defender Victor Lindelof inside the box.
Ayew elected himself to deliver but his feeble strike was pushed out by a stretched De Gea.
However, the Video Assistant Referee spotted the United No.1 was off his line when the kick was taken and so it had to be retaken.
This time Wilfried Zaha converted it into the roof to double Crystal Palace's lead.
Manchester United halved the deficit through new signing Donny van de Beek, who was making his debut, before Zaha scored again to regain their two-goal lead.