The winger made the gesture towards Marriner after being shown a yellow card for squaring up with James Ward-Prowse, only to be subsquently shown a second yellow for his reaction.
An FA spokesperson said: "Crystal Palace’s Wilfried Zaha has been charged following the game against Southampton yesterday [30 January 2019]. It is alleged his behaviour following a second-half dismissal amounts to improper conduct.
"The player has until 18:00 on 5 February 2019 to respond to the charge."
Zaha will now miss Crystal Palace's clash with Fulham on Saturday.
Of his player's dismissal, manager Roy Hodgson said: "It's disappointing that a player who perhaps provided the most entertainment throughout the game was consistently fouled," said Hodgson, who refused to criticise Marriner.
"That he wasn't able to contain his frustration with that consistent fouling and complains about a foul that wasn't given and probably should have been.
"I don't think he's targeted as a person I just think players who run with the ball as well as he does just get fouled. His play was good enough to provoke those fouls.
"It's not a good evening knowing he's going to miss the next game. We need him playing.
"We were fairly well in control. The first half performance was very good. Second half we should really have taken one or two of the chances that came our way."
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies