Leeds and Bolton have been fined £5,000 and £8,000 respectively with Wanderers boss Phil Parkinson fined £3,000 and given a two-match touchline ban after their league game on 23 February.
Both clubs accepted charges for failing to ensure their players conducted themselves in an orderly fashion.
The incident took place in the 69th minute of Bolton's 2-1 defeat.
Parkinson, who was sent to the stands, accepted a charge of misconduct in relation to his language and behaviour.
The Trotters manager will now miss their crucial home games against Millwall on Saturday and Sheffield Wednesday on Tuesday.
Bolton, who have lost their past three league games, are 23rd in the Championship and seven points adrift of safety with 11 games still to play.