Images posted on social media appeared to show Boca and Fluminense supporters clashing near the fan zone on the beach in Rio de Janeiro on Thursday.
Police used tear gas and rubber bullets during the fracas.
Three people were arrested after the brawl, the state's Military Police said, ahead of the final on Saturday in South America's equivalent of Europe's Champions League.
"Officers immediately surrounded the area, brought the situation under control, and two men -- Argentine tourists and a third man, Brazilian -- were taken to the 12th Police Station," police said in a statement.
CONMEBOL posted on X, previously known as Twitter: "CONMEBOL calls on the fans of Boca and Fluminense to share together the moments of joy and celebration that our football gives us. The values of the sport that we are most passionate about must be inspiring behaviours of peace and harmony. Therefore, we repudiate the acts of violence and racism that may occur within the framework of this final."
More than 100,000 Argentine fans are expected to travel to Rio, where there is also a Red Hot Chili Peppers concert this weekend.
The Argentine consulate in the city issued a list of warnings for travelling Boca fans, including: "Racist/Xenophobic chants and gestures constitute a serious crime that carries penalties of up to five years in prison.
"Avoid any type of provocation to the Brazilian people."
Rio's town hall has set up a special operation in an attempt to deal with the influx of supporters for Saturday's final.
Buenos Aires-based Boca, who have not won the Copa Libertadores since 2007, are looking to lift their seventh title in the competition on Saturday.
Information from Reuters contributed to this report.