Madrid are being investigated following the dismissal of Pepe after his challenge on Dani Alves saw him sent off. Mourinho was also removed from the touchline after he argued with referee Wolfgang Stark and his officials following the defender's red card.
Mourinho is also being charged in relation to his comments after the game, where he claimed that Barcelona were favoured by the Spanish authorities and Uefa.
He said: "It's clear that against Barcelona you have no chance.
"I don't know if it's the publicity of Unicef [the club's shirt sponsor], I don't know if it's because they are very nice, but they've got this power.
"I don't know if it's the friendship of [Spanish football federation president Angel Maria] Villar at Uefa, where he is vice-president.
"[Barcelona's Pep] Guardiola is a fantastic coach, but he's won one Champions League which I would be ashamed to win after the scandal at Stamford Bridge and this year, if he wins it again, it will be after the scandal at the Bernabeu.
"I hope that one day he will win a clean Champions League, with no incidents behind it."
Real are also being investigated following an alleged pitch invasion and the throwing of missiles from the crowd in the Bernabeu.
Barcelona’s charge relate to the sending off of substitute keeper Jose Pinto, who received his marching orders after a melee with Madrid players at half-time.