Real were thumped 5-2 in Jeddah, despite Barca having goalkeeper Wojciech Szczesny sent off on 55 minutes.
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In the post-match presentation, Florentino's words to Modric were caught by cameras.
"We have to lose a final at some point, right?" the Real Madrid president told the 39-year-old.
Modric later said at his post-match presser: "This is football and in football there are victories and defeats. We lost this time. It's never nice to lose, but if you have to choose a defeat, it's better in the Super Cup. You have to congratulate Barcelona, because they were better and that's it.
"It's not nice when your biggest rival scores nine goals against you in two games."