Ambulance officers were called to the prison, in Truganina, but were unable to revive the man.
Police also attended the scene and said the cause of death was not known but it was “not being treated as suspicious”.
A Corrections Victoria spokesman said it would be investigated by the state coroner.
“As with all deaths in custody, the matter has been referred to the coroner, who will formally determine the cause of death,” the spokesman said.
Port Phillip Prison, operated by security company G4S, is the biggest jail in Victoria and houses more than 1000 prisoners. Thirteen of those deaths had been in Port Phillip Prison, which has the state’s largest prison hospital unit for men.