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Barcelona were dominant in every aspect of the game and took advantage of three mistakes by Real Madrid to score.
Messi was sent off for the first time in his Barcelona career in the closing stages of extra time as they lost 3-2 to Athletic Bilbao.
Raul Garcia scored twice in a 2-1 win over Real Madrid on Thursday to knock the holders out of the Spanish Super Cup and set up a final against Barcelona.
Atletico's revival wrecked tournament organisers' dream of a 'Clasico' showpiece climax between Spain's most famous sides.
Real will meet the winners of Thursday's second semifinal between Barcelona and Atletico Madrid in Sunday's showpiece at the King Abdullah Sport City Stadium in Jeddah.
The victory maintains Zinedine Zidane's spotless record as a coach in finals. He has now led Madrid to success three times in the Champions League, and two each in the Club World Cup, UEFA Super Cup and now Spanish Super Cup.
Results 1-6
