Fans also went onto the Goodison Park pitch after Dominic Calvert-Lewin’s winning goal in the 84th minute.
“Everton have been charged with two breaches of FA rule E20,” said the FA.
“It is alleged that in the 84th minute and then following completion of the fixture, Everton FC failed to ensure that its spectators, and all persons purporting to be its supporters or followers, conducted themselves in an orderly fashion and refrained from using threatening and/or violent behaviour while encroaching onto the pitch area.”
During the pitch invasion after the game, Vieira appeared to aim a kick at a fan after being taunted by him.
Merseyside police spoke to both Vieira and the supporter and, along with the FA, took no actionover the incident.