A group gathering near the stadium in the city of Albacete chanted abuse about the 25-year-old, who has repeatedly suffered racism in Spain during games.
"Enough of this racism, it's completely shameful. It's not the image that represents the people of Albacete or the club," Albacete posted on social media.
Vinícius was named in Alvaro Arbeloa's starting line-up for the round of 16 cup game, his first match in charge as Real Madrid manager since the exit of Xabi Alonso.
In May 2025, five people received prison sentences in a landmark first ruling in Spain that condemned racist insults in a stadium as a hate crime after Vinicius was abused during Real Madrid's 2-0 victory over Real Valladolid in 2022.
There have been 18 legal complaints of racist behaviour against Vinicius since 2022. Real Madrid had no immediate comment on Wednesday's latest incident.
Vinicius has in the past expressed disappointment with what he describes as inadequate responses from governing bodies.