The final-day meeting between the four-time champions and Atletico Paranaense had to be suspended for an hour as military police were called in to break up supporter fighting.
Manoel scored a goal after just five minutes to put Atletico in front - a scoreline which would have seen four-time champions Vasco relegated.
Violence erupted within the stands just minutes after the goal, with riot police forced to use rubber bullets to break up groups of fighting fans and a helicopter used to airlift the injured to safety as the game was called to a halt.
TV footage showed an unconscious fan being repeatedly stamped on during the melee, while photographs of supporters bearing improvised weapons began to circulate on social media.
Atletico defender Luis Alberto was reduced to tears by the scenes, which come just two days after the draw for the 2014 World Cup group stages took place in the country.
"We are having a World Cup here next year. It's a shame that this kind of stuff still happens," Alberto told TV Bandeirantes. "I saw a fan being beaten until passed out. I've never seeing anything like this in my 20-year career"
A police presence was stationed outside the ground, but supporter safety within the Joinsville Arena was left to a private security firm.
"A football match like this usually demands 80, 150, 200 men working exclusively on it - men that we could be using elsewhere, taking part in other operations and protecting the city," a police officer explained to Radio Globo after being asked why police were not already inside the ground.
"These officers are taking care of other areas and we also have men on leave, because they have the right to take a day off and shouldn't end up losing those days off because of the matches," the officer said. "The police force allocated to the match is going to work exclusively outside the stadium. Inside, only private security hired by the teams."
The match was restarted more than an hour later.