Players and staff of both teams squared up to each other during second half stoppage time following a challenge by Leicester’s Ricardo Pereira on Chelsea’s Ben Chilwell.
Pereira and Leicester’s unused substitute Daniel Amartey, who courted controversy by throwing Chelsea’s pennant to the ground during the Foxes FA Cup final celebrations, were booked after the scuffle.
The FA have charged both teams for failing to control their players and have until next Tuesday to respond to the charge.
"Chelsea FC and Leicester City FC have both been charged with a breach of FA Rule E20.1 following their Premier League fixture on Tuesday 18 May 2021," a statement from the FA read on Thursday.
"It is alleged that both clubs failed to ensure their players and/or club officials conducted themselves in an orderly fashion and/or refrained from provocative behaviour during the 93rd minute.
"Chelsea FC and Leicester City FC both have until Tuesday 25 May 2021 to provide their respective responses."
Chelsea defeated Leicester 2-1 on the night to move up to third on the league table ahead of this weekend’s final round of fixtures.
The Blues are away to Aston Villa while Brendan Rodgers’ side, who slipped out of the top four after Liverpool beat Burnley on Wednesday, host beleaguered Tottenham Hotspurs.