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In the last track event of the evening, Gatlin would’ve been regarded as the favourite, despite the 150m being an unfamiliar distance for him.
But the American never really got going as Jobodwana – a 2015 world bronze medallist in the 200m – went toe-to-toe with the veteran coming into the bend.
After that, though, it was all Jobodwana as he put his foot down to speed away from Gatlin and the rest of the field – even having enough of a lead to raise his left arm in triumph in 15.08 seconds.
Gatlin – who only arrived in South Africa on Tuesday night – trailed in fourth in 15.23 as Roscoe Engel came through in second (15.17) and Luxolo Adams third (15.18).
Earlier in the evening, Caster Semenya also got the crowd cheering as she set a new South African record in the 1 000m with a time of 2:35.44.
Semenya had a pacemaker in 400m hurdler Wenda Nel, who went out too quickly though as she was well ahead of the 800m world champion.
But Semenya maintained her speed through to the end to break Ilse Wicksell’s previous mark of 2:37.2, set in 1983.
South African sprint star Akani Simbine was also victorious in the 100m, clocking a quick 10.05.