Staff and visitors were evacuated from a remand centre in Raven hall after clashes involving hundreds of inmates began at midday on Tuesday.
Heavily armed police stormed the prison in the early hours of the morning, according to the Victorian government.
The Corrections Department said the riot may have started because of a smoking ban in state prisons.
Several prisoners were hurt in the riot and were treated by medical staff, and two staff members suffered minor injuries, said prison authorities.