Kompany was also critical of Mourinho for using Eusebio's name as supposed proof that Benfica is not a racist club.
"Do you know what black players had to go through in the 1960s?" added the former Manchester City captain and Burnley boss.
"Was he (Mourinho) there to travel with Eusebio to every away game?
"Probably at the time the only option they had was to be quiet, to say nothing, be above it and to be 10 times better in order to get a little bit of credit for people to say 'actually, he is good'.
"That was Eusebio's life."
Mourinho has not directly addressed the criticism and spoke only to Benfica club media on Friday reflecting on the game and the aftermath.
"The game was truly demanding in every aspect," he said. "Up until the 50th minute, it was a great game, extremely demanding, both physically and tactically.
"But then, I also have to acknowledge, that from the 51st minute until now - and this won't end our conversation - it hasn't been easy to manage emotionally everything that has happened and continues to happen."
Kompany, who also spoke about racial abuse he experienced as a player, said talk of Vinicius' celebration should not distract from the player's immediate response to Prestianni's alleged remarks.
"I'm just thinking when Jose Mourinho is doing the knee slide at Old Trafford, when he does his celebration in front of the [Barcelona] fans in the Champions League semi-final with Inter Milan, when his Roma are playing Sevilla and he is fighting with the referee and the referee has to leave the country under protection," he added.
"I know 100 people who have worked with Jose Mourinho. I've never heard a person say anything bad about Jose.
"I understand he is fighting for his team and his club. You cannot be a bad person and have all the ex players you have had talk so positively about you.
"I don't need to judge him as a person but I know what I've heard. And I understand maybe what he has done, but he has made a mistake."
'He could have chosen his words better' - McCarthy on Mourinho
Meanwhile, former South Africa striker Benni McCarthy felt Mourinho should acknowledge he made a mistake with his "very wrong" comments.
"The situation, he could have handled it better or chosen his words better but emotions got the better of him," McCarthy told BBC World Service presenter Isaac Fanin.
"I know the statement he made was very wrong. But we're all human, we all make mistakes.
"When it comes from somebody I know personally and I know how he feels about our continent and our people and the players that play for him, he's the most stand-up guy that any African player will ever play for.
"I think it was an emotional decision, tough, where he maybe made a call and it wasn't the right call which he will later, hopefully come out and say that he made a mistake because that's what I would like to think, that's the kind of man he is."
Vinicius, who has been a victim of numerous incidents of racist abuse during his playing career, later said in a post on Instagram: "Racists are, above all, cowards."
Benfica have defended Prestianni and claim there is a "defamation campaign" against the Argentine.
The 20-year-old, who could face a minimum 10-match ban from European competition if found guilty, has denied directing racial abuse at Vinicius.