UEFA provisionally suspended Prestianni on Monday for one match after Argentine Prestianni was accused of insulting Vinicius during Real's 1-0 playoff first-leg victory in Lisbon.
Denying the accusation, Prestianni said the Brazilian misheard him, while Real's Aurelien Tchouameni said the Argentine told him he did not call Vinicius a "monkey" but directed a homophobic comment at him.
"It's just as serious because they are homophobic insults... I've also seen the images from the Benfica stand during the match, and I think it's deplorable to see that in a stadium," Courtois told reporters on Tuesday, referring to fans making monkey gestures.
"You may like a player more or less, but making those gestures is shameful... I haven't seen if they've said anything about going after their fans who made those monkey gestures.
"But with everything that has happened, there are many things that haven't been done well. I think that racism, homophobia - all of these things - we simply cannot accept them, and the insult is equally serious."
Courtois was also disappointed that Benfica coach Jose Mourinho said the fans were provoked by Vinicius' goal celebration.
"Vini didn't do anything wrong. He celebrated the way many opponents have celebrated against us, too," Courtois said.
"In the end, we need to move on and leave it at that. We can't justify an alleged act of racism with a celebration."
UEFA rules state 10-game suspension
UEFA rules state that "any person or entity that insults the human dignity of a person" on grounds including sexual orientation incurs a minimum suspension of 10 games.
The referee halted the game for 11 minutes after Vinicius complained, and Courtois said anti-racism protocols were getting better.
"In the end, the problem is that, in that moment, it was Vinicius who decided that we went back to playing. If Vini had said no, that he couldn't continue, then I think as a team we would have taken a stand there," Courtois added.
"Then, obviously, the other things that happened in the stands, for me, are reasons to stop a match and throw those people out.
"If it happens right in front of someone who is two metres away - a Benfica stadium security guard - then that person has to act and call the authorities... I think we can keep improving, and I think as a society we also need to stop being so foolish."
Real Madrid coach Alvaro Arbeloa said ahead of the second leg against Benfica in Madrid on Wednesday that Vinicius had shown "great bravery and character" since the alleged insult directed at him.
"Anyone in his situation, I don't know how I would react. He has always responded with courage, showing a huge personality and a lot of character... He is a fighter," Arbeloa said.
"He's very well, eager and motivated for these kind of games... He is a game-changing player. He is a leader, and we need him to get back to have fun tomorrow so he has a great match."