The tremor followed a massive earthquake in a fairly sparsely populated area of Botswana, about 240m north-west of Gaborone.
According to Ian Sanders from the Council for Geoscience the 6.3 magnitude quake's epicentre was at Sua Pan.
The tremor was felt in Zimbabwe, Mozambique, Durban, Pretoria, Johannesburg, Bloemfontein and Klerksdorp - the epicentre of another quake on Monday morning.
Johannesburg emergency services spokesperson Robert Mulaudzi said the tremor was felt around 19:45 on Monday evening. A building in Bree Street, and another at the intersection of Kruis and Commissioner Street were evacuated as a safety precaution.
No injuries were reported. Emergency services were on the scene.
Residents of Botswana wrote of their experience on the site earthquake-report.com.
"We felt the house was vibrating, all the window and door panels shaking heavily," wrote a resident of the city of Letlhakane.
A resident of the town of Jwaneng wrote: "Never seen a supermarket empty so quickly".
Residents of Gaborone reported feeling a strong tremor. Crockery was broken and pictures fell off walls. One resident reported all the dogs in the neighbourhood began howling.
No reports of the extent of the damage closer to the source were available immediately.
Earlier on Monday morning, residents of Klerksdorp, North West, and surrounding towns were woken up by a tremor. It was 2km deep and recorded around 05:08.
The Council for Geoscience’s Michelle Grobbelaar told News24 that in 2005 and 2014, the same region experienced magnitude 5.3 and 5.5 earthquakes.
Monday night's tremor was also felt in Klerksdorp. A resident told News24 it was less intense, but longer than the one in the morning.