Barcelona put in a clinical display to lift their first trophy in more than a year, having no silverware to show for last season.
Lamine Yamal, Robert Lewandowski, Raphinha and Alejandro Balde were all on target before halftime, after French forward Kylian Mbappe put Real in front in the fifth minute. Raphinha grabbed another in the second half while Rodrygo scored for Real.
Kylian Mbappe put Madrid ahead but a dominant Barcelona hit five in response before their goalkeeper Wojciech Szczesny was sent off in the second half.
LaLiga leaders Real recovered from that setback and are on a five-match winning streak ahead of defending the Super Cup in Jeddah, Saudi Arabia, but coach Carlo Ancelotti is cautious.
Jude Bellingham and Rodrygo scored second-half goals to help Real to a 3-0 win over Mallorca after Barcelona beat Athletic Bilbao 2-0 in the other last-four clash.
Flick's tactical approach, featuring an extremely high defensive line, also seemed ripe for Mbappe and Vinicius to pillage with their pace.
"Real Madrid strongly condemns any kind of behaviour involving racism, xenophobia or violence in football and sport, and deeply regrets the insults that a few fans uttered last night in one of the corners of the stadium," said Los Blancos in a statement Sunday.
"We are hurt, it's a tough moment, but I want to thank the fans for their support. We don't have to throw everything away, because there is nothing to throw away," added a downhearted Ancelotti.
The Catalan giants triumphed at the Santiago Bernabeu to snap Madrid's run of 42 matches unbeaten and continue their own revival under the German coach who arrived this summer.
Defending champions Real Madrid are set to host archrivals Barcelona in a LaLiga game at the Santiago Bernabeu tonight.
Kylian Mbappe's start at Real Madrid has been satisfactory, his performances neither spectacular nor underwhelming, but Saturday's La Liga Clasico offers the French superstar a springboard to kick on from.
The viral social media campaign before the September 29 clash encouraged Atletico fans to arrive at the club's Metropolitano stadium and utter "degrading and discriminatory insults with racist connotations" against a Real player, police said.
Real Madrid duo Thibaut Courtois and Rodrygo are likely to miss the Clasico clash with La Liga leaders Barcelona on Saturday with injury problems.
Pau Victor was the star of the night, scoring twice to lead Barça to victory in front of 82,154 fans, in what was also Hansi Flick’s first El Clasico as Barça manager.
Laporta demanded the Spanish football federation and the refereeing committee send Barcelona all footage of the incident and audio recordings of the officials' conversations.
The coach was furious after Lamine Yamal had a shot which Barcelona said crossed the line not given as a goal after officials could not prove that it had using VAR.
Jude Bellingham snatched Real Madrid a dramatic 3-2 Clasico win over champions Barcelona on Sunday to take them 11 points clear at the top of La Liga with six matches remaining.
The last chance saloon has opened its doors early for Barcelona as they travel to the capital on Sunday aiming to hold off Real Madrid's LaLiga title run in a desperate effort to stay alive in the race for the only remaining major silverware they can win.
Vinicius Junior struck a first-half hat-trick to fire Real Madrid to Spanish Super Cup glory in a thumping 4-1 win over rivals Barcelona on Sunday in Saudi Arabia.