Barnes was sent off for the incident, which triggered an automatic four-game ban as it was the player's second red card of the season, and the FA could now increase his punishment.
A statement read: "The FA has charged Brighton and Hove Albion's Ashley Barnes following his side's game against Bolton Wanderers on Saturday 9 March 2013.
"It is alleged that Barnes's behaviour in relation to the match official, for which the player was dismissed for violent conduct towards the end of the game, constituted an offence whereby the standard punishment that would otherwise apply was clearly insufficient."
Barnes must respond to the charge by 1800 GMT on Thursday.
Information from the Press Association was used in this report