Vinicius struck for the 1-0 Champions League play-off first-leg win, though his celebrations angered home fans. He was booked for his behaviour before he clashed with Benfica winger Gianluca Prestianni as they walked back to the centre circle.
The Brazilian reported what was said to the referee, accusing the Argentine of alleged racial abuse. The match was then suspended for 10 minutes as per UEFA protocols before it resumed as controversy swirled.
After the 1-0 defeat, Mourinho, who was sent off, said: "These talents are able to do these beautiful things, but unfortunately he was not just happy to score that astonishing goal.
"When you score a goal like that, you celebrate in a respectful way."
He also said: "Yes (Vinicius incited the Benfica crowd). I believe so. Then the words that they exchange Gianluca Prestianni with Vinicius, I want to be an independent."
Mourinho then went on, explaining what he told Vinicius during the match suspension: "I saw two completely different things. I want to be independent, and I don't comment about it. I told him exactly that.
"I told him - when you score a goal like that you just celebrate and walk back. When he was arguing about racism, I told him the biggest person (Eusebio) in the history of this club was black.
"This club, the last thing that it is, is racist. If in his mind there was something in relation to that – this in Benfica. They told me different things. But I don't believe in one or another. I want to be an independent.
"There is something wrong because it happens in every stadium.
"A stadium where Vinicius plays something happens, always.
"Look, I am saying it was a good 50 minutes of football. I believe millions of people are watching around the world - a crazy goal and then game over."