An Antoine Griezmann double had Barca leading heading into injury time but a late concession coupled with Inaki William's brilliant winner in the additional 30 minutes was enough to send the Catalan giants to defeat.
Messi had been on the edge of much of the contest in any event, but his sending off for lashing out with his hand showed his frustration with how Barcelona had thrown the match away. It was his first red card in a Barcelona shirt and as he trudged off, the referee barely had enough time to blow the whistle and announce Athletic the champions.
But who were the best and worst players on the pitch?
✔️ GOOD PERFORMANCE
Iker Muniain: 8.4
The little wide man's delivery into the area was a constant thorn in the side of Barcelona throughout the contest.
His cross found the head of Asier Villalibre in the dying moments to force extra-time, putting it in a position where his team-mate couldn't miss, then slipped the ball into Inaki Williams' feet in extra-time to curl home a brilliant effort.
Beyond that, his cross saw a Raul Garcia header harshly ruled out for offside, while another ball landed on a plate for Villalibre, but he couldn't convert. An optimum example of delivery from wide, and Barca couldn't handle him.
❌ BAD PERFORMANCE
Ousmane Dembele: 6.1
He wasn't great against Real Sociedad in midweek, and he wasn't great here either, and Dembele continues to test the patience of even his biggest fans.
He saw plenty of the ball and, as usual, had an electric display of pace to offer, but the end product just isn't there and he seems to have been more wasteful than ever in this Supercopa mini-tournament.
Barca need a player with pace, given Ansu Fati's continued absence, but Dembele is doing more harm than good in their attacks at the moment.
⭐ STAR MAN
Antoine Griezmann: 9.4
It's fair to say that the Frenchman hasn't had the best of times in a Barcelona jersey, but he proved for the first time here that with him and Lionel Messi on the pitch at the same time, he can be the difference maker.
For his first goal he pounced on a loose ball that broke inside the area and fired low with his left foot into the bottom corner with style.
And for the winner he linked well with Jordi Alba, running onto the left-back's pinpoint low cross to convert into the net.
He made 67 touches - a level of involved higher than he usually has, completing two dribbles and hitting four shots, three of which was on target. We could be witnessing the turning of the tide for Griezmann at Camp Nou - it's a shame his team-mates couldn't support him on this occasion.