The Real Madrid striker was shown a straight red card on Saturday for a nasty challenge on Antonio Blanco in their 1-0 win at Alaves.
Mbappe has since been handed a one-match ban by the RFEF, leaving Yuste stunned.
He snapped on RAC-1: "I would say that it is absolutely absurd.
"A very hard foul, which could have caused a fracture, an injury. If it had happened to one of our players, which will not happen because our players are clean, I don't know what would have happened."
He then added: "If one of our players had attacked an opponent in that way... It's unfair. It reiterates that we all have to do more because this is a bad example for football. It's a disgrace."
Barca players angry after last night
Meanwhile, on Barca surviving Borussia Dortmund's fight-back last night to reach the Champions League semifinals, Yuste added: "This is a winning team.
"Hansi (Flick), his staff and Deco are winners and hungry for titles. We achieved our goal of reaching the semifinals, but these are people who strive for excellence. And I think critical thinking is key.
"This team wants to win titles, and you can only improve if you are hungry and angry when you lose."