He was moving on soon enough and with what now looks like infinite prescience it was in the direction of the new juggernaut, Bayern Munich.
Fabregas, chided by the Nou Camp crowd that had already been pushed to the edge of despair by the absence of Lionel Messi, must have felt more than ever a captive of fate. Bayern's 3-0 victory was not so much another exhibition of relentless power and control as the annihilation of a football culture.
That culture, some always felt, was raised too high too quickly, but the extent of its fall was no less dramatic for that. The aggregate margin of 7-0 was huge and cruel but it only told half the story.
Among the debris Fabregas certainly had reason to believe that if great talent often shapes the most significant careers, so does timing.
Guardiola, who takes command from 67-year-old Jupp Heynckes at the end of what is beginning to resemble one of football's great campaigns, has only one smudge on a horizon that looks on the face of it to be utterly untrammelled.
How does he improve on a team that, apart from any other achievement, can claim to have ushered one of the great sides in club football down from the mountain top?
But were Barça really the unanswerable claimants to the title of the best ever, more formidable, more enduring than the likes of the Real Madrid of Di Stefano and such other contenders as Milan, the old Bayern, Liverpool and Ajax?
Sir Alex Ferguson hinted so much, certainly, after his Manchester United was ransacked at Wembley two years ago. He said that his rival Guardiola should think very carefully before walking away. "Sometimes you get only one chance to work with a set of great players like Messi, Iniesta and Xavi," he said. "Such an opportunity may never come again."
That was a theory not so easy to discount in the bowels of Wembley Stadium but tonight it seemed like nothing so much as a wisp of passing football theory.
This was especially so when Arjen Robben scored a goal of exquisite judgement and craft early in the second half. It made the withering demand on Barça to score six goals for a place in their fourth Champions League final in seven years. Such an arrival was never more than the remotest possibility after the destruction that came to them in the Allianz Arena, and what Robben's strike also made unlikely was the possibility that Barça would retrieve at least a fragment or two of pride.
That was the last ambition of Guardiola's successor Tito Vilanova, for whom the best perspective could only be his survival after months of fighting for his health. Before the game, and despite his knowledge that the world's best player would not be able to join the battle for redemption, he declared: "We believe we can fight back. It is our obligation and we are convinced it is possible. We know it's very difficult but we are Barça and we can never give up, especially when we have 90 minutes to play at home."
It was a brave resolve but you only had to look at the haunted face of Vilanova as he hunched in the dugout to understand the degree of the failure – and its meaning.
The reality, which was underlined by the ferocious force of Bastian Schweinsteiger and the hunger of a Robben who has known much disappointment at this exalted level of the club game, was that this was not so much a defeat as a thunderous reallocation of football power.
When Gerard Pique smashed the ball into his own net in the face of another powerful, streamlined Bayern attack, the extent of the reappraisal of Barça's place around the top of the game could hardly have been greater.
Messi, no doubt, will reappear in all his superb skill and ingenuity and, who knows, there might be a little life in the fabled tiki-taka that was supposed to have conquered the football in unprecedented style.
Of course it hadn't because of course the game moves on, always, and when Thomas Müller made the great ground seem ever more like a mausoleum of dead dreams with another goal, there was no question about which game, which teams, were the new vanguard.
It was the football of the Bundesliga, of Bayern Munich and their beautifully inventive rivals Borussia Dortmund, who arrive at Wembley this month not so much to play a final but introduce us more deeply to the latest new football, the latest new age.
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