Two of the fans were arrested for a "racial slur" having allegedly directed monkey chants at Corinthian fans during Tuesday night's Copa Libertadores last 16 clash. The third fan was arrested for "racism" and "apology for crime" for having allegedly raised his arm in a Nazi salute.
Sao Paulo's security ministry said in a statement that all three were "caught red-handed" at the Neo Quimica Arena in Brazil's largest city and spent the night in police cells, where they remain.
The first two face between one and three years in prison if found guilty. Their bail was set at 20,000 reais ($3,850), the inspector in charge of the case told CNN Brasil. The third fan, for whom no bail was granted, faces between three and six months in jail if found guilty.
Two months ago, another Boca fan was arrested in the same stadium for making monkey chants when the two sides met in the Libertadores group stage. Boca were last week hit with a $100,000 fine by South American football's governing body CONMEBOL for racism by their fans last month at their Bombonera stadium in Buenos Aires in yet another match against Corinthians.
Tuesday night's first leg ended goalless with the return in Buenos Aires next Tuesday.