The Real Madrid forward has been subjected to frequent racist abuse this season and Brazil decided the friendly was a good opportunity to strike back as the match was staged in Espanyol's stadium near Barcelona.
In a powerful move Brazil abandoned their iconic yellow and green shirts and were instead kitted out in an all-black strip in a stand against racism for the first half of the game.
The Brazilian Football Confederation was behind the gesture accompanied by the slogan of "Com racismo nao tem jogo" (With racism, there is no game).
Vinicius himself, wearing the number 10 shirt, got on the score sheet with an 88th-minute spot-kick, by this time kitted out in Brazil's usual colours.
Newcastle forward Joelinton was well placed to tap in the opener on the goal-line on 27 minutes while Rodrygo curled home the second two minutes later.
Stuttgart striker Serhou Guirassy pulled a goal back with a close-range header on 35 minutes but Eder Militao restored the two-goal lead shortly after the restart rising high to meet a cross at the far post.
Manchester United midfielder Casemiro escaped with a yellow card for a late tackle on Francois Kamano that was at odds with the party atmosphere in the stadium.
Late in the game Brazil substitute Malcom was brought down in the box and Vinicius was urged to take the penalty, which he hit hard and low enough to beat 'keeper Ibrahim Kone who had dived the right way.
Earlier in the week the Spanish and Brazilian football federations presented their plan for a friendly match at the Santiago Bernabeu in March 2024 to combat racism following global outrage at the abuse of Vinicius Junior.
