The players clashed in the 95th minute after referee Michael Oliver had awarded a free-kick to Spurs, with Andy Carroll adjudged to have fouled Fernando Llorente.
Carroll, Llorente, Winston Reid and Eric Dier were booked for their part in the melee and both clubs will now have to answer an FA misconduct charge.
An FA statement read: “West Ham United and Tottenham Hotspur have been charged by The FA following their fixture on Saturday [23 September 2017].
“It is alleged that in or around the 95th minute of the game, both clubs failed to ensure their players conducted themselves in an orderly fashion.
“They have until 6pm on 28 September 2017 (Thursday) to respond to the charge.”
Tottenham claimed a 3-2 victory over their London rivals, despite being reduced to 10 men in the 70th minute when summer signing Serge Aurier received a second yellow card.