Leeds and Bolton have been charged by the Football Association following a melee during the Sky Bet Championship match at Elland Road on February 23, while Trotters boss Phil Parkinson also faces separate disciplinary action.
Parkinson was sent to the stands following a scuffle involving both sets of players shortly after Ezgjan Alioski's freak goal had restored Leeds' advantage midway through the second half.
The home side, who are chasing promotion to the Premier League, eventually won 2-1.
A statement from the FA issued on Wednesday morning read: "Leeds United and Bolton Wanderers have been charged following their EFL Championship fixture on Saturday (23 February 2019). It is alleged that they failed to ensure their players conducted themselves in an orderly fashion during the 69th minute.
"In addition, Phil Parkinson has also been charged with misconduct in relation to his behaviour in the 69th minute.
"Both clubs and the Bolton manager have until 18:00 on 01 March 2019 to respond to the charge."
Parkinson boss blamed the flashpoint on Leeds midfielder Mateusz Klich spraying water down Joe Williams' back in the aftermath of the Bolton player's foul on Alioski.
Speaking after the match, Parkinson was left baffled by referee Tony Harrington's decision to show him a red card.
"There was a melee on the side of the pitch – one of their players has poured a drinks bottle over one of our player's head," Parkinson said.
"Both sets of staff have gone to separate it because they didn't want it to escalate into anything. I did have a go at (Leeds defender) Pontus Jansson saying I felt he'd instigated it by running over.
"There were about 15 people in amongst it being calm and he (referee) has decided to pick me out and give me a red card."
