West Ham were pressing for an equaliser in stoppage time when players from both sides started an on-pitch altercation, prompting the charge.
Andy Carroll and Winston Reid were booked in the 96th-minute incident along with Fernando Llorente and Eric Dier from Spurs.
A statement from the FA read: “West Ham United and Tottenham Hotspur
“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 September 28, 2017 to respond to the charge.”
in 2015 West Ham and Chelsea were fined £40,000 and £50,000 respectively by the Football Association following a similar charge of failing to control their players in a game the Hammers won 2-1.