Moments before Bilbao’s momentous triumph was confirmed, Messi threw an arm at Asier Villalibre, who had earlier scored a 90th-minute equalizer in normal time to deny FC Barcelona victory.
Antoine Griezmann’s double looked to have sealed the trophy but Villalibre intervened before Inaki Williams’ fabulous strike three minutes into extra time proved decisive.
Lionel Messi shook off a thigh problem to start in Seville and was required to play all 120 minutes as FC Barcelona attempted to take the game to penalties.
Instead, the 33-year-old lost his temper at the end of a combative contest, reacting to a late challenge from Villalibre by swiping his hands across the back of his opponent.
It meant a first ever red card for Lionel Messi in 753 appearances for Barcelona, to go with his two reds for Argentina in 2005 and 2019.
“After so many years in football, Leo knows perfectly well when he is fit to play,” said FC Barcelona coach Ronald Koeman.
“We talked, and he said he was in a good place to start. He has survived the game, given the maximum, nothing more.”
Lionel Messi’s anger will take some limelight away from Bilbao, who had already denied the competition a Clasico final by beating Real Madrid in the semi on Thursday and now have completed the set.
It means a title and the perfect start for Marcelino Garcia Toral, who only took over as coach less than two weeks ago.
But there was praise too for his predecessor Gaizka Garitano, who oversaw this team reaching the Copa del Rey final last season, which earned qualification in the first place.
“This is for Gaizka Garitano and his coaching staff as well who brought us here,” said Williams.
Organizers at the Spanish Football Federation might have hoped for the global attraction of a Clasico, especially as the coronavirus pandemic had already kept the tournament in Spain rather than the lucrative Saudi Arabia, where it was played last year.
Yet this was a frantic final, with an astounding result.
FC Barcelona arrived on the back of a nine-game unbeaten run and a trophy, even a minor one, would have turned encouraging signs in recent weeks into more tangible evidence of a revival under Koeman.
“It is not a step back,” he said “Always winning titles is helpful to show that we are on the right track, but it is only one game, it is a Super Cup, and we will show in the next few games that we are on the right track.”
Bilbao were the better side in the first half, more decisive in possession and more aggressive out of it. But both teams created little for 40 minutes and then in two minutes both had scored.
A brilliant pass created each of them, Lionel Messi the instigator for FC Barcelona.
He collected from the right and threaded through for Jordi Alba on the left, whose cut-back was intended for the Argentinian but spilled out to Antoine Griezmann, who could not miss.
Marcelino hurled his water bottle to the ground in disgust, but his team were soon level.
Williams played the pass, his clipped ball over the top catching Alba off-guard, with Oscar De Marcos sneaking in and half-volleying home.
Raul Garcia thought he had his third goal in four days when he headed in just before the hour but FC Barcelona survived.
With 10 minutes left, Antoine Griezmann struck again, Alba’s cross evading the Bilbao defence and finding the Frenchman, who steered in at the front post for what looked like the winner.
Instead, Bilbao scored in the 90th minute to send the game to extra-time and then the 93rd to lead for the first time.
Villalibre was allowed to volley in from close range but there was little Barcelona could do about Williams’ effort, the striker cutting inside from the left and whipping a tremendous shot into the top right-hand corner.
Unai Nunez might have sealed it but failed to connect. Antoine Griezmann almost rescued it but fired high on the volley with his right foot.
Then Villalibre left a shoulder in on Lionel Messi, who reacted, scuttling after his opponent and swinging an arm around the back of his head. Lionel Messi and FC Barcelona were beaten.