Deon Hotto slotted the winning kick in the shootout after Emmanuel Mbola had fired over the crossbar for Chipolopolo, who will now compete in the Plate section of the competition.
Zambia started the game brightly, as Jackson Mwanza forced a sharp save early on from Maritzburg United goalkeeper Virgil Vries.
Vries was on hand again to foil a stike from Mamelodi Sundowns midfielder Mukuka Mulenga shortly before the interval.
At the other end, AmaZulu's Sadney Urikhob wasted a promising chance late on, while Vries pulled off another fine stop at the death to ensure the teams were deadlocked inside regulation time.
Zambia XI: Kennedy Mweene, Donashano Malama, Christopher Munthali, Emmanuel Mbola, Aaron Katebe, Justine Zulu (Paul Katema 69’) , Kondwani Mtonga, Jimmy Ndhlovu, Jackson Mwanza (Allan Mukuka 43’), Mulenga Mukuka, Bornwell Mwape (Patson Daka 47’).
Namibia XI: Virgil Vries, Denzil Haoseb, Willem Mwedihanga, Chris Katjiukua, Ananias Gebhardt, Peter Shalulile (Willy Stephanus 79’), Ronald Ketjijere, Petrus Shitembi (Heinrich Isaacks 88’), Deon Hotto, Benson Shilongo, Wangu Gome.