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Simon Magakwe became the first South African to break the 10-second barrier in the 100 metres when winning the national title at the weekend.
The 27-year-old clocked 9.98 seconds at the University of Pretoria to claim his sixth victory in the event.
Magakwe and Johan Rossouw had shared the previous record of 10.06 established 26 years ago.
Second-place Akani Simbine (10.02) also bettered the old mark during the championships that doubled as qualifiers for the 2014 Commonwealth Games in Glasgow.
Meanwhile: World record-holder Wilson Kipsang won the men's London Marathon in a course record two hours, four minutes and 29 seconds..
Kipsang's smashed the previous London set by fellow Kenyan Emmanuel Mutai in 2011 by 11 seconds.
It was a second London victory for Kipsang, the 2012 champion, who outpaced compatriot Stanley Biwatt in the finishing straight.
Last year's winner Tsegaye Kebede of Ethiopia was third ahead of compatriot Ayele Abshero.
Kenya celebrated a race double as Edna Kiplagat won the women's event.
