Another fantastic footballing spectacle between arguably the best two sides in Europe was again overshadowed by the antics of Mourinho, who appeared to put a finger in the eye of Barca assistant Tito Vilanova during a melee in the closing stages.
Vilanova responded by striking the Portuguese on the side of the head as the match - which saw Barca emerge 3-2 winners on the night to claim the Supercopa 5-4 on aggregate - finished in ugly scenes at the Nou Camp.
The latest news about the Spanish Supercopa fallout
Yet with reports from Spain suggesting the incident involving Mourinho and Vilanova was not mentioned in the referee's report, it is likely that both will face no further sanction from Spanish football's governing body.
Barca central defender Gerard Pique said following the game that Mourinho, who will this season serve a touchline ban in Champions League fixtures after comments made about Barca during similarly ill-tempered clashes between the two arch rivals last term, was "destroying Spanish football" and Vilarrubi has also hit out at the former Inter Milan boss.
"Expanding on Pique's comments, I must say that Mourinho is a blight on Spanish football," said Vilarrubi, the vice-president of the institutional area at Barca, was quoted as saying on radio station RAC1.
"I'm convinced that Madrid as an institution cannot support their coach in some cases like yesterday [Wednesday], so we'll see what happens in the coming hours."
It remains to be seen what, if any, punishment Mourinho will receive for his actions, but Vilarrubi wants the Portuguese to be brought to task.
"I don't know exactly who, but someone has to act on this matter and I hope that they do it."
Mourinho, meanwhile, continued his verbal assault on Barca following the match, labelling the European champions "a small team".
He was particularly unhappy that the ball-boys appeared to disappear after half-time with the home side 2-1 up on the night and 4-3 ahead on aggregate.
"Real Madrid gave a spectacular performance from the first to the last minute," he said.
"We came here to play. What I'm about to say is not a criticism, I'm just stating a fact: there were no ball-boys in the second half, which is something typical of small teams when experiencing difficulties.
"I'm not going to say we're happy because we didn't win the Spanish Super Cup, that would be hypocritical of me.
"But we intended to play like men and not fall on the ground at the slightest touch.''
The sub-plot came at the end of a wonderful game which saw Barca twice take the lead through Andres Iniesta and Lionel Messi with Cristiano Ronaldo and Karim Benzema replying.
But, with extra-time looming, Barca won it when Messi volleyed home Adriano's right-wing cross.
Madrid's frustration then spilled over with Marcelo sent off for a crude tackle on debutant Cesc Fabregas, on from the bench, which sparked a bust-up that saw Mourinho's clash with Vilanova and red cards for substituted players David Villa and Mesut Ozil.
Pique was clear in his opinion on where the blame lay, saying: "I do not talk about the brawl. But it's a shame, it is not the first time and it's always the same.
"Someone has to take action on the matter. Mourinho is destroying Spanish football. There is talk about the Catalans, but the problem is with Madrid.
"I think it's going too far. It cannot always end well. In the end this will end very badly."
Barca midfielder Xavi added: "Madrid's image was shameful. The pictures speak for themselves. We believe in footballing justice and justice was done today [Wednesday]."
Mourinho's opposite number Pep Guardiola did not wade into the issue but had a word of caution for those involved in the tense atmosphere on the pitch.
"We must be careful, because one day we will cause harm, not on the field but off, and we're all a little responsible for this," he said.