A sterile filling machine and related method are provided for sterile filling a container with a substance. The container includes a resealable stopper or portion and a chamber for receiving the substance therein. The sealed, empty containers are subjected to radiation capable of penetrating through the resealable portion and chamber for sterilizing the container. The previously sterilized containers are then transported through another sterilizing chamber, such as an e-beam chamber, to sterilize the penetrable surface. A filling member is moved into engagement with the resealable portion to pierce the sterilized penetrable surface of the resealable portion and inject the substance through the filling member and into the chamber of the container. Energy is then transmitted onto the stopper to hermetically re-seal the penetration in the resealable portion.