The Portuguese took responsibility for his side's 2-1 loss at the Bernabeu and revealed he would look at the incident involving his controversial central defender.
After Cristiano Ronaldo's early strike was wiped out by Carles Puyol's header and an Eric Abidal winner, Madrid left the pitch to jeers from its frustrated fans. But Mourinho gave little importance to that reaction, and instead took the blame for the loss.
"I always understand [what is going on in the crowd] but I never listen, either before or after [a game]," the Portuguese coach mused.
"The responsibility is mine, especially when my team loses. Victory has many fathers; defeat only one. I've been in football a long time and I understand this.
"The cup final victory we all celebrated, but in defeat I am the only parent."
Mourinho also revealed Pepe could be punished if he is found to be guilty of stamping on Lionel Messi.
Pepe, playing in midfield, had already been booked for a cynical foul on Sergio Busquets early on and could have been dismissed as he clearly stamped on Messi's hand with just over 20 minutes remaining.
But the referee failed to spot the incident and Pepe went unpunished.
Barca coach Pep Guardiola claimed he had not seen the incident, but said the television images spoke for themselves. Straight afterwards, Mourinho told reporters that his player could be punished.
"I have not seen what Pepe did," he claimed. "I have to watch it. Pepe did a great job for the team but if something happened, I didn't see it.
"However, if it was intended, obviously, it is punishable."
Ronaldo's performance is already the subject of much debate, with the player's influence having waned after his early salvo.
However, Mourinho was again quick to defend his compatriot, declaring, "My view is that Cristiano was the best player on our team."
As for his side's hopes of turning things around at Camp Nou next Wednesday, Mourinho admitted, "The tie is still open but difficult, if not very difficult."
Madrid returns to La Liga action this weekend versus Athletic Bilbao, while Barca travels to Malaga.