Real and Barca face UEFA hearings
Real midfielder Pepe and Barca reserve goalkeeper Jose Manuel Pinto will also face hearings after being shown red cards in the semi-final first leg, European football's governing body said following a petulant semi-final first leg.
The Madrid club will have to explain incidents of missile-throwing and a pitch invasion during their 2-0 defeat at the Bernabeu, UEFA said.
Mourinho, Pepe and Pinto will all miss Tuesday's second leg as they serve automatic one-match bans which could now be extended by UEFA.
Pepe was sent off for a studs-up lunge at Barcelona's Daniel Alves in the second half and Mourinho was ordered from the bench for his complaints over the same incident.
Pinto was ordered off for his part in a scuffle at the entrance to the players' tunnel at halftime.
UEFA said the hearing would take place on May 6.
Mourinho bitterly criticised the referee after Wednesday's match and said Barcelona had "great power."
Mourinho has already been in trouble with UEFA this season, seving a one-match ban over allegations that two of his Real Madrid players engineered deliberate red cards in a group game with Ajax Amsterdam.