South Africa, fifth in 1999 and 2005, amassed 10 medals including five golds over the five-day championships.
They started the final day with a 1-2 in the men's 200 metres, won by Retshidisitswe Mlenga in a season's best time of 21.03.
The 17-year-old Mlenga, who already held the best time at altitude of 21.14secs, held off compatriot Tshenolo Lemao in a reverse result to the men's 100m.
"I came in very focused, having made a mistake in the 100m finals that happens to be my favourite race," said Mlenga.
"I listened to my coach's instructions this time, and I am happy to have won the gold medal."
Lemao, who won South Africa's first ever gold in the 100m, took silver in a personal best 21.12 while Germany's Luis Brandner (21.23) was third.
China finished second in the medals table on five gold, two silver and four bronze with Cuba in third on eight medals - five gold, two silvers and a bronze.
