Tigre were losing 2-0 after a feisty first half, and two of their players - Paulo Miranda and Gaston Diaz - were red-carded in a half-time brawl.
However, the Argentine side accused private security officials and Brazilian police of pulling guns on the players in the dressing room and did not return to the pitch to play the final 45 minutes, allowing the referee to crown Sao Paulo as champions.
"They pulled two guns on us, the rest of the match is not going to be played," Tigre coach Nestor Gorosito told Fox Sports.
"They ambushed us and one of them pulled out a revolver and put it against [goalkeeper] Damian Albil's chest. Their security and police also hit us, there were around 20 of them."
Sao Paulo president Juvenal Juvencio stoked the flames after the match by claiming that Tigre fled instead of backing up Gorosito’s assault claims.
"They were going to lose by a big score," he told the club's website. "Our biggest victory is the fact that the Argentines ran away."
The opening strike came from Lucas Moura, in what was his farewell game for the club ahead of his January transfer to Paris Saint-Germain.
With World Cup 2014 less than 18 months away, Brazilian footballing officials will be keen to ensure situations such as this do not occur when 31 other nations from around the globe visit South America.