A system handles the sterilization of thin-body, pouch-type, flexible containers (1) and provides for applying sacrificial closures (200) to the pouches. The system loads the provisional closed pouches to be sterilized on a transport device (300) for collective transport, to perform the sterilization of the transport device (300) carrying the provisional closed pouches. The system separates in a sterile chamber, the sacrificial closures (200) from the pouches, performing filling and applying an inviolable cap (100).