Wolfgat, named after the geological and archaeological caves in the fishing village of Paternoster, also won an award for the best "off-map destination".
It’s head chef, former food blogger Kobus van der Merwe, is the reigning San Pellegrino and Acqua Panna Chef Of The Year.
The World Restaurant Award judges grade establishments on excellence, integrity and diversity.
The judges include René Redzepi of Denmark’s Noma Restaurant, cookery writer Yotam Ottelengi and Ulster chef Clare Smythe, who is the first woman in Britain to win three Michelin Stars.
“Without even looking at the pictures of Wolfgat – the whitewashed cottage, the golden sand – our inspectors’ report makes you want to book a flight to Cape Town and drive up to Paternoster in a hurry," said the judges.
“The place is super simple, rustic and yet perfectly elegant. We sat by the fireplace. We could watch the fishermen go out, come back and empty the catch from their brightly coloured boats.”
'Keep it small, keep it sustainable'
Situated in a 160-year-old Cape Dutch fisherman’s cottage, Wolfgat can seat only 20 diners. Van der Merwe says “by keeping it small, I keep it sustainable.”
He serves lunch from Wednesday to Sunday and dinner on Friday and Saturday.
His seven-course meal costs 53 euros.
He won points for his Strandveld menu – which translates from Afrikaans as beach and field – emphasising sustainability and creating jobs for locals.
He employs six people, mainly woman, to forage for local herbs – known as veldkos, or field food – and seaweed from rock pools which is served together with produce from his garden on the day it is picked.
It accompanies his dishes of seafood, lamb and local venison.
Van der Merwe says his dishes are inspired by spicy Cape Malay flavours and he concentrates on sustainability. He tries to interfere as little as possible with the products and serves them pure, raw and untreated.
“I am really proud to bring something like this to our continent and beautiful country,” he said of the award. "I am very proud to be working with a team of mainly women.”
“I don’t feel worthy to be here," he told AFP. "My staff who go out every day gathering herbs, succulent and dune spinach should be here…. It’s their baby.”