The incident occurred during Real Madrid's 1-0 victory in midweek, with Vinicius scoring the decisive goal. The match was briefly halted after the Brazilian reported alleged racist abuse from Benfica winger Gianluca Prestianni - an accusation the Argentine has strongly denied. UEFA has since opened an investigation into the matter.
In the aftermath, Mourinho - who was sent off late in the game - criticised Vinicius' goal celebration, describing it as "disrespectful", and cited club legend Eusebio as evidence that Benfica is not a racist institution.
While Bayern Munich coach Vincent Kompany labelled Mourinho's remarks a "huge mistake", it was McCarthy - who played under Mourinho at Porto and won the 2003/04 Champions League - who offered a more personal and measured response.
Speaking to the BBC World Service, McCarthy acknowledged that his former manager had erred but urged perspective.
"The situation, he could have handled it better or chosen his words better but emotions got the better of him," McCarthy said. "I know the statement he made was very wrong. But we're all human, we all make mistakes."
McCarthy, who has frequently spoken about issues affecting African players, was quick to defend Mourinho's character, particularly regarding his relationship with players from the continent.
"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," he added.
The former striker stressed that leadership is ultimately defined by accountability, expressing hope that Mourinho would publicly clarify his position.
"I think it was an emotional decision 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. That's what I would like to think. That's the kind of man he is."
Vinicius, who has previously been subjected to racist abuse during his career, later posted on Instagram: "Racists are, above all, cowards."
Benfica have defended Prestianni and described the situation as a "defamation campaign", while the player himself has denied directing any racial slur at the Real Madrid forward. If found guilty, he could face a significant suspension from European competition.
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Benfica manager Jose Mourinho has sparked controversy after claiming that Real Madrid's Vinicius Jr provoked both players and fans following his match-winning goal in Tuesday night's Champions League play-off first leg in Lisbon.
