Xabi Alonso took up his favourite position at the Camp Nou, easing into a seat in the stands and looking silently out across the pitch, feet up, job done. It was some time after Real Madrid had won the Copa del Rey semi-final second leg 3-1 against Barcelona, the clock ticking towards midnight, and the Camp Nou was quiet. The stadium had been emptying for a while, ever since Raphaël Varane headed Real Madrid's third; by the time Jordi Alba scored Barcelona's only goal in the 88th minute, there were not that many fans left to celebrate and those that were still there did not much feel like doing so.

If Alonso took it all in, it was difficult for Barcelona fans to do the same. Difficult for their players too. In little over a week, they have been beaten by Milan in the Champions League and knocked out of the Copa del Rey by their greatest rivals. Alonso sat outside, not saying a word. Down the tunnel and up again, past the chapel and to the left, other players were giving their views. Cristiano Ronaldo was beaming, socks pulled up to the knees, cap on backwards, Varane too. And through the doors, Iker Casillas, who had not played, was giving the official press conference: another victory for José Mourinho.

Xavi Hernández was trying to put a positive spin on events. "We have lost the least important of the [three] titles," he said. On one level, he was right and Barcelona will win the league. But he was also very wrong: Barcelona have lost far more than the least important title. They have lost identity and supremacy, fitness and confidence. They are a team that have been beaten before; what makes this different is that this time they have been well beaten, so deservedly defeated. The cover of AS shouted: "Toma, toma, toma!" Take that, and that, and that! Sport called it "a painful knockout".

Clásicos have a habit of feeling definitive somehow, of giving way to sweeping judgments and bold calls, of eras ending. Often it is an exaggeration but for Barcelona the problems were evident on Tuesday night and it was hard to avoid the conclusion that they were about more than just one night.

For all Barcelona's possession – 63% – they rarely looked like scoring. La Vanguardia called the game a "debacle" and Barcelona "impotent". "Humiliation" is a word being used a lot. Marca saw the tables turning. For all that Madrid's counterattacking style is often treated in Spain as if it is somehow cheating, it proved devastating, again. Barcelona proved impotent, again.

Writing in El Mundo Deportivo, Santi Nolla noted: "For the first time in the past few years Madrid were better than Barcelona in more than just the score."

"Real Madrid are better [than Barcelona] now," ran the headline in AS.

They would say that, wouldn't they? Maybe, but they're right. In October, the league game finished 2-2 at the Camp Nou, which is impressive in itself but it goes deeper: over the past six clásicos Madrid effectively claimed last season's league title in Barcelona, won a Spanish Super Cup over two legs, and have now reached the Copa del Rey final on 18 May (or 17 May, or 19 May or 22 May, depending on what happens now, what with 18 May being the night Eurovision is on ... but that's a story for another day).

"If the objective in hiring Mourinho was to slay the dragon, mission accomplished," wrote Juanma Trueba of AS on Wednesday morning.

As for the other debate, that has tipped very clearly in Ronaldo's favour: on Tuesday he alone had more shots on target than the entire Barcelona side. Messi did not have one. The Portuguese has now scored on his past six visits to the Camp Nou. "Checkmate" ran the headline in El País, Ramón Besa describing Ronaldo as "football's emperor". He continues: "The No7 was better than the 10, the man whipping a disfigured and dethroned Barcelona side."

Mad Madridista Tomas Roncero was enjoying it. "We'd been waiting a long time for a moment like this; it was about time divine justice put everyone in their place," he writes. "Those same people who a month ago said how bad Madrid were are now beating a retreat, asking what the devil is going on. I'll tell you: Madrid have the best player in the world." He concluded: "Madrid danced on Barcelona's tomb."

Sport's cartoon has Barcelona's fans reaching for their medical cabinet: anti-depressants for today, Viagra for tomorrow. The front cover headline reads: "We have to get up again." For Barcelona, the mission is to work out what is wrong and to resolve their problems fast. Milan are on the horizon. But can they? As El Mundo Deportivo's cover put it, there could be "no excuses".

"The reality is the reality," said El Periódico. "There was a lack of ideas the like of which we had never seen before, miles from what this team was until very recently." Sport was asking questions, frantically seeking an answer. Why don't they learn from their mistakes? Why is there no spark? Why did [David] Villa come on so late?

For the first time, questions are being asked about the impact of Tito Vilanova's illness. There has been a certain discomfort in talking about it before – it feels a little unfair, grubby and insensitive, when the coach is in the United States undergoing chemotherapy for cancer and when Jordi Roura is effectively thrust into a role he did not seek – but on Tuesday it was there. Talk of Barcelona not needing a coach, an agenda pushed until quite recently, is this morning picked apart by Santi Giménez of AS; time to recognise the importance of Pep Guardiola and Vilanova. "It's not true that anyone can manage this team," he says. "I know that's opportunistic, but it's my turn."

Roura himself insisted that he has no desire to be anything other than the assistant manager. He also put forward an explanation of his own: Barcelona may be suffering a physical dip, a product of training that aims towards certain peaks throughout the year, that relative February drop in fitness and freshness is normal and Barcelona tend to recover in March and April. The risk this time is that, by then, with the league already won, there is nothing to recover for.