The Portuguese duo have both been punished for their part in the ugly scenes at the end of Real Madrid's 2-1 loss to Atletico Madrid last week.
Mourinho was sent to the stands during the eventual 2-1 loss to Atletico Madrid after remonstrating with the officials over a decision on the pitch.
While he will be allowed to take his place on the Blancos bench for the final two fixtures of the Liga season, he could be banned from the touchline for two cup ties if he makes his move to Chelsea, should the FA choose to enforce the ban.
Ronaldo, meanwhile, was sent off late on for aiming a kick at the face of Atleti captain Gabi and will miss his side's first two Copa games next season.
Madrid finished the campaign without a trophy thanks to the loss to the club's city rival last Friday and Mourinho's departure from the Spanish capital was confirmed on Monday.