The last South African champion was Kroonstad-born David Gatebe in 2013.
Gongqa finished in 03:09:43 with Warinyane Lebopo of Lesotho second in 03:10:21.
The pair were neck-and-neck for much of the last six kilometres before Gongqa pulled away to secure victory.
Gongqa and Lebopo were the sole survivors of a group of 10 runners who broke away from the pack after 42 kilometres.
Another Lesotho runner, Teboho Sello, was third with Zimbabwe’s Collen Makaza fourth and Melly Kennedy, a Kenyan, fifth.
Belarusian Maryna Damantsevich won the women’s race in 03:37:13.
Damantsevich hit the front early in the piece and was helped by Caroline Wöstmann’s withdrawal after 11 kilometres with a hamstring injury.
Wöstmann was bidding for a hat-trick of Two Oceans victories.
Lesotho’s Namakoe Nkhase won the men’s half-marathon in a race record time of 01:03:15.
Irvette van Zyl was the first woman in the half-marathon and 39th overall.
Of the total entries of 11 000 for the ultra-marathon, 4 005 were novices, 7 782 were men and 3 218 women.
In the half-marathon, which drew 16 000 entries, men numbered 7 426 and women 8 754.
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