The Spaniard had also described Marriner as not having the best record with Newcastle's players "in terms of red cards".
The FA said in a statement on Twitter on Tuesday that Benitez had been charged for his pre-match comments about the referee and had until 6:00 p.m. BST (1700 GMT) on Friday to respond to the charge.
Newcastle held Palace to a 0-0 draw in the match.
(Reporting by Simon Jennings in Bengaluru)
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