UEFA provisionally suspended Benfica winger Gianluca Prestianni for one game as its investigation into the incident, which saw him cover his mouth with his shirt and allegedly make a racist comment.
Prestianni denied the accusation of racism, claiming the Brazilian misheard him, as the club and manager Jose Mourinho made statements backing him this month.
Asked about the comments from his former Chelsea manager, Courtois stated that it bothers him that society is so stupid.
"Mourinho is Mourinho and, as a coach, you'll always defend your club," he said.
"But it bothers me that Vinicius' celebration is being used against him.
"Vini didn't do anything bad. He celebrated the same way many rivals have celebrated against us.
"It happened, and we can't justify a suspected act of racism because of a celebration. I think we have to be less stupid as a society."
UEFA said further punishment could be handed out once that investigation is completed, but it will be hard to slap Prestianni with a punishment after he covered his mouth, as the act is not clear.
Real Madrid beat Benfica 1-0 away from home and the two sides will clash once more on Wednesday night.
Prestianni will miss the game, but Vinicius Jr will be able to start as he aims to lead his side to the next round.