Barca won the first-leg semi-final match at the Bernabeu 2-0 thanks to two late Lionel Messi goals after Madrid had been reduced to 10 men in the 61st minute when Pepe was shown a straight red card for a challenge on Dani Alves.
In the post-match press conference, Mourinho was far from happy and his comments could lead Barca to make an official complaint to UEFA's disciplinary committee.
A statement on www.fcbarcelona.com on Thursday morning read: "There will be an 'extraordinary' meeting of the board at 1700 to discuss the action to be taken after the events of the Bernabeu.
"Later there will be a press conference at 1900.
"At the press conference after the game, Real Madrid coach Jose Mourinho harshly criticised referee Wolfgang Stark and suggested Barcelona receive favourable treatment.
"The Legal Services of FC Barcelona are considering reporting the Real Madrid coach to the Disciplinary Commission of UEFA."
The Real Madrid coach said: "Josep Guardiola is a fantastic football coach, but he has won one Champions League which would embarrass me 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."
The first 'scandal' Mourinho was referring to was the Champions League semi-final between Barca and Chelsea in 2009, when the Catalan club progressed through to the final following a controversial second leg in London.
Andres Iniesta's injury-time strike earned Barca an away-goals win, but at the final whistle Chelsea's players confronted referee Tom Ovrebo, who had waved away at least four penalty appeals during the game. Barca would go on to beat Manchester United in the final.
Mourinho, who last season saw his Inter Milan side reduced to 10 men in the second leg of their Champions League semi-final at Barca but still progressed through to the final, did not stop there either in his post-match rant on Wednesday night.
He added: "Today [Wednesday] it's clear that against Barcelona you have no chance.
"His accusations of Barca were more than that: 'I don't know if it's the publicity of UNICEF [on shirts], I don't know if it's the friendship of [Spanish football federation president Angel Maria] Villar at UEFA, where he is vice-president, I don't know if it's because they are very nice, but they have got this power. The rest of us have no chance'."
"Why couldn't Chelsea reach the final two years ago? It was a miracle that Inter reached the final last year.
"I am here just to ask this question and I hope to get the answer one day."
Regarding the match itself, Mourinho believes it is now "mission impossible" for his side to progress through to the final.
However, Barca boss Guardiola is not assuming the tie is already over heading into next week's second leg at the Nou Camp.
"We are a step away from the final, but we will carry on respecting Madrid, very, very much," said Guardiola, who refused to respond to questions about Mourinho's comments.
"If we start to believe we are already through, Madrid can punish us. We don't believe we are already there [Wembley]."