The fourth division game between Gama and Botafogo of Sao Paulo was halted towards the end of the first half when Botafogo fans arrived late, accompanied by supporters of Gama's arch-rival Brasiliense, according to terra.com.br, a popular news portal.
The ensuing scuffles caused the game to be held up for several minutes to ensure the players were safe, Globo added.
The game ended in a 0-0 draw.
The stadium in the capital Brasilia is often used by teams from other cities in a bid to keep it from becoming a white elephant.
Local teams Gama and Brasiliense have small support bases and only 3,115 people were in the 73,000 capacity arena for Sunday's game.
In the first division, Atletico Mineiro remained in top spot after winning their sixth successive game, beating Ponte Preta 2-0 on Saturday.
The four teams behind them all won, with a last–minute goal from Fred helping second-placed Fluminense beat Atletico Paranaense 2-1.
Fluminense signed Ronaldinho Gaucho on Saturday but he is not expected to make his debut until next month.
Corinthians hammered a hapless Flamengo 3-0 at the Maracana on Sunday to leapfrog over Gremio into third spot on goal difference, even though the southern side also won, beating Vasco da Gama 2-0 on Saturday.
Fifth-placed Sao Paulo beat Coritiba 3-1, with former AC Milan striker Alexandre Pato getting a brace.
At the bottom, Joinville lost their ninth game out of 14 to stay rooted to the foot of the table, one point behind Vasco and Coritiba.
(Editing by Greg Stutchbury)
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