Spurs won the London Stadium clash 3-2, but after being three-nil up before a Hammers resurgence, tensions were high in the dying minutes.
And with the match winding down, and the visitors still leading, a number of players were involved in a melee, prompting the charge.
A statement from the FA read: “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.”
Harry Kane had put Spurs into a two-goal lead before Christian Eriksen added a third.
Javier Hernández and Cheikhou Kouyate were on target for West Ham before referee Michael Oliver cautioned Andy Carroll, Winston Reid, Andre Ayew, Eric Dier and Fernando Llorente following the late altercation – which started after a tackle by Carroll.
Both clubs have until 18:00 BST on Thursday to respond to the charge.