Brazil's Superior Court of Sporting Justice ruled on Friday that hosts Atletico Paranaense must play 12 home games at least 100km from their home city of Curitiba and six of them must be behind closed doors.
Opponents Vasco da Gama, who were relegated after losing the match, must play eight games outside Rio de Janeiro, four of them behind closed doors.
Atletico were also fined 140,000 Brazilian reais ($59,900)and Vasco were fined 80,000 reais.
The fighting was a huge embarrassment for the hosts of next year's World Cup and came days after world governing body FIFA said some stadiums had missed an initial deadline to be ready.
Atletico, playing in a rented stadium while their own arena is being refurbished for next June and July's showpiece, were 1-0 up in Sunday's game when fights broke out in the stands.
The match was halted for more than an hour as hooligans ran riot and a police helicopter landed on the pitch to ferry one injured fan to hospital. Four people were seriously hurt.
The game, which marked the end of the Brazilian season, eventually restarted and Atletico won 5-1.
"The repercussions and the seriousness of what happened made such a punishment inevitable," Atletico's lawyer Domingos Moro told reporters.
Both clubs said they will appeal the decisions.
(Writing by Andrew Downie; reporting by Rodrigo Viga Gaier; Editing by Mark Meadows)
