"I have never been racist with anyone and I regret the threats that I received from Real Madrid players," the 20-year-old Argentina forward, who faces a potential 10-match ban if found guilty of racial abuse in UEFA's disciplinary code, said on X.
The European soccer governing body said Wednesday it has appointed a special investigator to gather evidence.
Benfica said Prestianni was the victim of a "defamation campaign."
The Champions League playoff game at Benfica's Stadium of Light was halted for nearly 10 minutes on Tuesday after the referee initiated the anti-racism protocol, which is the standard procedure when a player alleges being abused.
Cameras picked up Vinícius telling French referee François Letexier that Prestianni called him a "monkey."
FIFA President Gianni Infantino said he was "shocked and saddened to see the incident of alleged racism" and praised the referee for activating the anti-racism protocol.
"There is absolutely no room for racism in our sport and in society," Infantino said on X. "We need all the relevant stakeholders to take action and hold those responsible to account."
Benfica showed support for Prestianni on Wednesday, with the Portuguese club claiming that Madrid players who said they heard the insult were too far away.
Benfica later released a statement saying it welcomed UEFA's investigation and that it "fully supports and believes the version presented" by Prestianni, "whose conduct while with the club has always been guided by respect" toward everyone.
Benfica fans had reacted angrily to Vinícius celebrating his 50th-minute goal by dancing by the corner flag, throwing bottles and other objects toward the Madrid players.
Prestianni then confronted Vinícius and said something while covering his mouth with his jersey.
Madrid, who won 1-0, host the second leg on February 25 with the overall winners advancing to the round-of-16 in European club soccer's top competition.
After the match, Vinícius posted a photo on Instagram of him celebrating by the Benfica corner flag. He wrote: "Racists are, above all, cowards. They need to cover their mouths with their shirts to show how they are weak.
"Nothing that happened today is new to me in my life and in my family's life. I was shown a yellow card for celebrating a goal. I still don't know why."
Prestianni insisted that Vinicius misunderstood what was said, while Benfica players after the match reportedly said the Argentine provoked the Brazil forward but never racially insulted him.
"I want to clarify that at no time did I direct racist insults at the player Vinícius Júnior, who unfortunately misinterpreted what he thought he had heard," Prestianni said.
He did not say why he covered his mouth.
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