Seydou Keita and Luis Fabiano struck for the hosts midway through the first-half against a Real team which lost Sergio Ramos for two yellow cards five minutes after halftime.
"Where's the referee from?" asked a clearly furious Schuster after the match. "He's Catalan? That says it all. I won't say anything else."
The German also said: "You can't compare Valencia and their situation with tonight's Sevilla. The media always talks about the previous game, but there's no comparison.
"The first person in charge is the team - and that's Sevilla. They won 2-0, there's nothing else to say."
Real Madrid sports chief Pedja Mijatovic later emerged to claim of being abused by Sevilla fans as he and fellow directors watched the game.
Mijatovic barked: "When we came, we knew that we were going to have an atmosphere that was against us. Everything has culminated with our destroyed bus. I cannot begin understanding it.
"They have been insulting us in the director's box, I have never experienced such a situation."