The punishment only applies to matches organized by the Brazilian football federation, meaning the teams will be allowed to play at home during the regional championships that start next month.
Because of the sanctions, Atletico Paranaense will likely have to delay its debut in the Arena da Baixada, its new stadium being built for the World Cup.
The match last weekend was being played in Joinville instead of Atletico's base in Curitiba because it had already been punished because of fan violence.
Hundreds of fans from both teams charged against each other in the stands, throwing punches and kicks and using sticks and metal bars in the fighting that left four people injured, including a man who had to be airlifted from the pitch.
The disturbing images from the fight quickly made their way around the world, raising doubts about Brazil's preparedness to host the World Cup next year.
About 80 private security officers were separating the rival fan sections at the Arena Joinville, and the fighting only ended after police arrived firing rubber bullets to disperse the fans.
World Cup organizers have said a similar problem is very unlikely to happen during football's showcase tournament next year, when several hundred security guards are expected to work at each match. Nearly 900 worked at Confederations Cup matches this year. They also claim that the dangerous fan groups common in club matches will not be among the World Cup crowd.
The tribunal on Friday also said the local federations and the match referee were not at fault for the incidents in Joinville.
Vasco da Gama, which was relegated after losing the match 5-1, wanted the result annulled because the referee did not follow regulations when he waited 73 minutes to restart the game after the brawl. Tournament regulations say the maximum time is 60 minutes. But the sports tribunal denied the team's request on Thursday, meaning the club will have to play in the second division for the second time in five years.
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