In Rome it was simpler. You massacred a good chunk of the men, and enslaved the rest along with the women and children. Very important figures such as the defeated king would be temporarily spared to walk in the victorious general's triumph.
There was only one state prison in ancient Rome - the Carcer at the foot of the Capitoline hill. It's lower chamber (the Tullianum) was used for executions, and even the term 'prison' is misleading as it was neither intended nor used for long-term incarcerations. This is where Jugurtha was held after he had been defeated by Marius. He walked in chains in Marius' triumph, then was executed (104 BC). Enemy leaders were generally garroted.
This much later coin, based on a seal Sulla wore after the Social War, shows Sulla 'defeating' Jugurtha. It was part of his later anti-Marius propaganda, and does not in any way reflect reality or what people thought at the close of the second century. At the time, although Sulla captured Jugurtha with the help of king Bocchus of Mauretania, he was simply seen as acting as Marius lieutenant by the Romans [Sallust 113.6]:
Jugurtha came to the same place unarmed and with only a few followers, as had been agreed, and immediately on a given signal those who were in concealment rushed upon him from all sides at once. His companions were killed; the king himself was bound and delivered to Sulla, who took him to Marius.
Julius Caesar also held Vercingetorix (left) in the Cerca before again marching the Gaul in his triumph, then executing him.
Important 'guests' of Rome were literally housed as guests of important Roman peers, albeit under house arrest. They were hostages though, not prisoners or enemies defeated in battle.
Because Saints Peter and Paul were traditionally held here, one upper level was turned into S. Pietro in Carcere during the Medieval period