Inspired by teenager Gavi, who scored and set up goals for Robert Lewandowski and Pedri Gonzalez, the Catalans produced one of their best performances in years against their bitter clasico rivals.
Having enjoyed great success as a player at Barca, Xavi returned in November 2021 and after a summer of heavy spending this emphatic victory is a sign his project is moving in the right direction.
Karim Benzema netted a late consolation for Madrid, who have been far from their best since the World Cup break and also fell three points behind Barcelona in La Liga last weekend.
Madrid coach Carlo Ancelotti suffered his first defeat in a final since 2014, with Los Blancos surrendering the trophy they earned last season to Barcelona, who have now won the Super Cup a record 14 times.
"We knew it was a chance we had to take, we have lived through an era of changes at the club and in the dressing room, and this will reinforce us to keep fighting for more titles," Barca captain Sergio Busquets told Movistar.
"You know how [Gavi] competes, he's very young. Most players at his age would be in the youth team and he's playing at an incredible level, giving assists, getting goals.
"He has a brilliant future ahead of him and a lot of room to improve. I hope he's a player who marks an era at Barca."
Xavi crucially used four central midfielders with Gavi, 18, drifting inside off a nominal starting position on the left and frequently giving Madrid right-back Dani Carvajal the slip.
Toni Kroos played as Madrid's deepest midfielder with Aurelien Tchouameni out injured, and he was overrun.
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Madrid goalkeeper Thibaut Courtois made a brilliant early save to deny Lewandowski, tipping his low drive against the post, while Benzema headed narrowly off-target.
Barcelona broke the deadlock when Busquets pressed well after a loose Antonio Rudiger pass, leading to Lewandowski feeding Gavi, who slotted home confidently.
Pedri and Ousmane Dembele were also involved in an exchange of slick passes before Lewandowski teed up Gavi, whose clever run went untracked.
Gavi turned provider for the second, running on to De Jong's pass and sliding the ball across for Lewandowski to finish clinically.
The Catalans' dominance brought back memories of their 4-0 win over Madrid at the Santiago Bernabeu last season, which had been the highlight of Xavi's time in charge, until now.
Gavi, who won the Golden Boy award in 2022, was the game's outstanding performer and showed Barcelona are in good hands now and for years to come.
Madrid's own young star Vinicius Junior was shackled by Ronald Araujo, the Uruguayan playing at right-back to directly subdue the Brazilian's threat.
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Courtois denied Dembele after a brilliant Alejandro Balde run and the overworked Belgian stopper was keeping Madrid's slim hopes alive.
By contrast, Barcelona's Marc-Andre ter Stegen went untested until the 70th minute, when he collected a long-distance Kroos effort, by which time his side had netted their third.
Lewandowski released Gavi, who crossed for Pedri to tap home at the back post as Barcelona romped to a compelling victory.
Pedri, 20, also won the Golden Boy award, in 2021, and is another emblem of the maturing young talent at Xavi's disposal.
The only blot on Barcelona's copybook was a late Benzema strike, finishing after his first effort was blocked.
"We have to learn. It's a difficult moment and that's it," Ancelotti told Movistar.
"We don't have to do too much. We knew before the game the team wasn't at its very best.
"The game exposed some weaknesses. It's a blow. We have to recover and prepare for the next game."
The biggest blow for Madrid may prove to be the morale boost the victory has given their rivals.
Although Xavi will ultimately be judged on his performance in major competitions, and Barcelona have already been eliminated from this season's Champions League, he will take heart from this victory.