With Everton leading 1-0 shortly before half-time at Goodison Park, Kevin Mirallas went in heavily on West Ham's Morgan Amalfitano.
That challenge prompted an angry reaction from a number of the visiting players, with James Tomkins confronting Mirallas, who pushed the defender in the chest.
Tomkins went down holding his face, before tempers were eventually cooled, Everton going on to win 2-1 courtesy of Leon Osman's strike.
On Wednesday, the FA released a statement confirming that both clubs had been charged for their part in the fracas.
"Everton and West Ham United have been charged by The FA following their game on 22 November 2014," the statement read.
"It is alleged that in or around the 40th minute of the fixture, both clubs failed to ensure their players conducted themselves in an orderly fashion.
"The clubs have until 6pm on 1 December 2014 to respond to the charge."
