The Springbok Sevens side edged England 19-12 to win the first leg of the series in Dubai.
A Robert Ebersohn try ensured South Africa went to an early lead and a further score by Mpho Mbioyozo took the advantage to 12-0 at half-time. England had few opportunities and were well marshalled by the Bok defenders.
Tom Biggs hit back straight after the break to give England a sniff. The momentum shifted and when Paul Delport was yellow carded the Boks looked in trouble.
Mickey Young crossed for an English try and the conversion saw the scores tied at 12-12. But Gio Aplon made a late break and was under the crossbar before passing to Ryno Benjamin. Fortunately Benjamin held on and the title was secured.
In the other divisions Samoa beat Kenya 12-7 to win the Plate, while Portugal thumped France 40-0 to win the Bowl. USA took the Shield honours by beating Arabian Gulf 31-7.