A cap system for permanently sealing a pharmaceutical vial having an interior, an opening to the interior of the vial and a flanged neck surrounding the opening, the flanged neck having an undersurface, said cap system comprising a closure assembly comprising: an elastomeric stopper having a body portion and a plug; a retainer member comprising a top wall and a peripheral sidewall, said sidewall comprising a periphery and plural resilient fingers located about the periphery of said sidewall, said plural resilient fingers comprising tabs for holding said elastomeric stopper within said retainer member; and a locking cap member comprising a peripheral sidewall including inwardly projecting lugs, said locking cap member being slidably coupled to said retainer member; said stopper being arranged to be secured to the vial so that said plug enters into an opening of the flanged neck to partially close the opening of the vial, said retainer member being arranged to be secured to the vial with said fingers of said retainer member being arranged to flex over the flanged neck of the vial and then snap into engagement with the undersurface of the flanged neck of the vial and with portions of said top wall of said retainer member in engagement with portions of said stopper to hold the stopper in place on the vial to seal the opening in the vial and prevent removal of said stopper from the vial, said locking cap member being arranged to be slidably secured over said retainer member after said retainer member has sealed the opening in the vial to lock said locking cap member in a fixed position with respect to said retainer member, whereupon said inwardly projecting lugs of said locking cap member apply an inward force on said fingers to ensure that the vial is permanently sealed. an elastomeric stopper having a body portion and a plug; a retainer member comprising a top wall and a peripheral sidewall, said sidewall comprising a periphery and plural resilient fingers located about the periphery of said sidewall, said plural resilient fingers comprising tabs for holding said elastomeric stopper within said retainer member; and a locking cap member comprising a peripheral sidewall including inwardly projecting lugs, said locking cap member being slidably coupled to said retainer member; said stopper being arranged to be secured to the vial so that said plug enters into an opening of the flanged neck to partially close the opening of the vial, said retainer member being arranged to be secured to the vial with said fingers of said retainer member being arranged to flex over the flanged neck of the vial and then snap into engagement with the undersurface of the flanged neck of the vial and with portions of said top wall of said retainer member in engagement with portions of said stopper to hold the stopper in place on the vial to seal the opening in the vial and prevent removal of said stopper from the vial, said locking cap member being arranged to be slidably secured over said retainer member after said retainer member has sealed the opening in the vial to lock said locking cap member in a fixed position with respect to said retainer member, whereupon said inwardly projecting lugs of said locking cap member apply an inward force on said fingers to ensure that the vial is permanently sealed.