Hosts Oman sorely missed its star rider, the injured Hamood al Dughaishi, on the concluding day.
The sultanate team didn't win any medal on Friday and took the overall silver, while Sudan won the bronze medal.
A total of ten teams competed over four days in eight disciplines and at the end, South Africa finished on top with 758.5 points.
Oman had 693.5 points and Sudan collected 654.
South Africa's Johan Jordaan, who won a gold in the individual sword event, was adjudged the best rider of the World Cup.
On Friday, South Africa won the team sword event, with Egypt taking silver and Yemen bagging bronze.
Later in the day, Egypt claimed the gold in the Indian File event and was followed by runner-up Iraq and then Sudan.
Patrick Vorster, the South African Tent Pegging Association's chairman and leader of the South African delegation, said, “It is a happy and proud moment for us, to emerge as the world champions. It will definitely be a boost to the sport in our country. The riders worked together well and executed the plans to perfection.”
H E Sheikh Saad al Saadi, the Minister of Sports Affairs, presented the winner's trophy and other awards. Also present on the occasion were Mohammed Issa al Fairuz, the International Tent Pegging Federation (ITPF) chairman, Sayyid Mundhir al Busaidi, the Oman Equestrian Federation (OEF) chief, ministers and other dignitaries.
Fairuz told Muscat Daily, "The event was a grand success. All the teams praised the organisational aspects of the World Cup. The OEF and the sports ministry did a splendid job to organise the first World Cup. The event has laid a strong foundation for future success. Oman has set a high standard and the future events need to be only better than this one.”
Fairuz said the ITPF's executive committee has agreed to host the World Cup every two years and added that Yemen will host an international competition in October.