A downpour early Sunday left the green on the par-3 fourth waterlogged and only 17 holes will be used in the final two rounds at Durban Country Club, reducing the course to a par-69.
Four-time winner Ernie Els took a two-shot lead over Retief Goosen going into the final day.
Rain had already delayed the 100th edition of the event.
The European Tour and South Africa’s co-sanctioning Sunshine Tour said the decision was not unprecedented, pointing to two occasions at the Dutch Open in the late 1960s when anti-apartheid protesters had dug up a green and the event was played over 17 holes.
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