Barcelona issued a statement giving their reaction to Mourinho's comments.
"In the post match press conference, Jose Mourinho severely criticised the referee Herr (Wolfgang) Stark and insinuated that UEFA treated Barca favourably," the club said.
"The club's legal department is now studying whether to take his remarks to the UEFA disciplinary commission."
Later the Catalan club confirmed it had decided to pursue the matter with UEFA over Mourinho's "inappropiate comments".
"The motivation behind this complaint comes from the wish of the (club) president (Sandro Rosell) to defend the club's history and prestige, its members, its managers, its players and its directors," Barca spokesman Jordi Freixa explained.
He continued: "It is absolutely inacceptable that someone can call into question our history, our titles..."
As well as the Mourinho affair, UEFA said it was also investigating the throwing of missiles by Real Madrid fans at the Santiago Bernabeu, a pitch invasion and the red card shown to Real defender Pepe on the hour mark for a tackle on Dani Alves.
The dismissal of Mourinho will also be discussed at the hearing on Friday week.
UEFA are also looking into the red card handed out to Jose Pinto, Barcelona's reserve goalkeeper, who received his marching orders following the half-time fracas on the touchline.
AFP