Vasco - four-time Brazilian champions - needed to win to give them hope of avoiding relegation from Serie A but, with with Atletico winning 1-0, trouble in the stands forced the referee to stop the game after 17 minutes.
The match had already been moved to Joinville following previous problems between the clubs' supporters, but switching to a neutral venue was not enough to prevent further altercations.
Fans from both clubs charged at each other in the stands with punches and kicks being aimed at each other, and reports from Brazilian television station Globo Esporte suggest at least three fans were hospitalised.
With players distracted by the events on the terraces - and the intervention of security official Ricardo Marques Ribeiro - the fixture was halted.
Following lengthy discussions, military police were brought into the stadium and the game was able to resume 70 minutes later.
