The home side have an overall lead of 159, but suffered a massive blow when they lost in-form Quinton de Kock on the last ball before the interval, caught and bowled by Suranga Lakmal.
South Africa had won 19 of 21 previous home series against Asian opponents, with the only exceptions being when India and Pakistan shared one series each.
The win gave the tourists a 2-0 series triumph after they clinched the first test in Durban by one wicket in Durban last Saturday.
Watch the first one-day global between South Africa and Sri Lanka live on Sky Sports Cricket from 7.55am on Sunday, 3 March.
Sri Lankan leaders congratulate cricket team for Test series win against South Africa Sat, Feb 23, 2019, 08:45 pm SL Time, ColomboPage News Desk, Sri Lanka.
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Bernd H Knöller, the head chef and owner of RiFF, said he's working with officials to figure out what happened. Her husband and son were also taken ill, but are said to be recovering, according to reports by The Guardian .
"A lot of the guys here are not in the ODI team and they've under-performed, I can't know what they are thinking, but for me the World Cup was not in my mind at all, I was extremely motivated to do well here". "It's not easy when you come to South Africa and to win a series 2-0, it's a lot of hard work".
Opener Lahiru Thirimanne (29) provided a caught and bowled chance for Duanne Olivier, who took three for 61, before Rabada removed nightwatchman Rajitha. Yet the Sri Lankans heeded the call of Dimuth Karunaratne, who was announced as "interim" captain, to "compete in every session" and to play with a smile on their faces.
As upsets go, this defeat of South Africa will rank right up there especially after the Sri Lankans came to country having been thumped by both Australia and New Zealand earlier in the southern hemisphere summer. Fernando, meanwhile, hit 10 fours and two sixes in his 106-ball knock. He said the defeat was "up there with the most disappointing" of his career.
Sri Lanka had resumed on the third morning on 60 for two, though effectively three down with spinner Lasith Embuldeniya out of the test with a broken thumb, and as has been the case through the series looked to attack the home bowlers.
Hashim Amla (32) provided some resistance before he edged part-time spinner Dhananjaya de Silva (3-36) to slip, while skipper Faf du Plessis (50 not out) ended the innings as top-scorer but ran out of partners.
Sri Lanka's cricket team celebrates winning their two five-day cricket tests against South Africa.