The prisoners had clambered onto the roof of the Alcacuz penitentiary near the northeastern city of Natal.
An AFP video reporter filmed the inmates standing for hours with flags on the partly destroyed red tile roof before police chased them down.
Officers also fired rubber bullets at relatives who had crowded in front of the entrance to the prison, an AFP journalist saw.
A total of 26 prisoners were killed in Alcacuz - many of them beheaded, officials said yesterday - in a violent riot that broke out Saturday night.
On Sunday, police had stormed the prison and ended the uprising.
It was the third major massacre to hit Brazil's overcrowded jails this month, all of them thought to involve suspected drug gangs.
Officials said two rival gangs clashed in the overcrowded Natal jail.
Separately the state government said prisoners rioted early yesterday morning at another jail in the Raimundo Nonato prison, also in Natal.
No one was hurt or escaped in that riot, which was quelled by police, it said.
A further 33 died in a riot in Roraima state on January 6.
The Natal massacre which erupted on Saturday raised fears that the wave of violence could spread across the country.
"Authorities are playing a dangerous game by underestimating the scale" of the crisis in the prison system, said Renata Neder, a human rights adviser to Amnesty International in Brazil.
The rights watchdog yesterday called for an independent inquiry into the killings.
President Michel Temer said on Twitter that the federal government stood ready to provide "all assistance necessary" to quell the prison unrest.
Prisoners had cut off the electricity and were said to have firearms.
The prison was built for a maximum of 620 inmates but currently houses 1,083, the state justice department said.
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