The riot broke out before dawn at the Aparecida prison complex, where nine inmates were killed and around 100 escaped in Monday's uprising.
A spokesman for the prison system said no one was killed and no inmates escaped in the latest incident, which was put down in less than three hours by special forces and military police troops.
Authorities had not completed its tally of the injured, the spokesman said.
The toll was much higher in Monday's uprising. Inmates burned to death and others were decapitated in the clashes between two rival criminal gangs. Fourteen inmates were injured.
Three days later, a riot broke out in the same area of the prison, but resulted in no casualties, according to media reports.
Extreme overcrowding has produced explosive conditions in Brazil's prisons.
The country has the world's third largest prison population with 726,712 inmates as of June 2016 but has capacity for only 368,000, according to the most recent official statistics.