When Real's players celebrated Eder Militao's opener in the 64th minute, Atletico ultras Fondo Sur, who are located in the south lower stands, threw objects at Belgian Courtois, who alerted the referee, with the match temporarily halted.
The game resumed after a delay of more than 20 minutes and Angel Correa equalised deep into added time in the 1-1 draw, after which the Atletico players went towards the south stands and applauded the ultras, which was heavily criticised.
Simeone had to weather the current storm after he said on Sunday that players "must be responsible" and "take it easy while celebrating" because "people get angry"
His remarks suggested that Courtois' gestures towards the ultras caused the problems and that players who behave in such a manner should be punished.
"The other day I didn't shut up, I said something many see. I received millions of messages thanking me for what I said, many are represented in that situation," he told reporters ahead of Wednesday's Champions League match at Benfica.
"If it is up to me, I sanction the one who provokes from the place he has as a protagonist. Now society is very sensitive and we need firmness."
Despite saying he was misinterpreted, Simeone insisted he would not change anything he said.
"I am doing good and I'm calm because I am clear and up front, I like to say what I feel. I wouldn't change anything I said," added the Argentine.
"I have said three times that I condemn violence, showed rejection of the aggressors, said that as a club it was a great opportunity to show outwardly what should be done.
"Then I gave an opinion that they twisted and took wherever they wanted. I think it is good for football if that debate is opened up. The other day it was Courtois' turn but it could have been someone else. But people stop at what they want.
"I said one thing and then I gave an opinion and many took the opportunity to have fun between Monday and Tuesday, but now we are thinking about Benfica."
Atletico said on Monday that they had banned a person identified in the throwing of objects and were working with police to identify others, who will also be disciplined.
