The earthquake hit the city in the early hours of Sunday, June 11.
According to the US Geological Survey, which records earthquakes around the world, the quake happened at 2.38 am local time.
It said the epicentre was 6 kilometers (3.7 miles) from Alberton, a town on the southeastern outskirts of Johannesburg.
Reports say the tremor was widely felt not only within the city but also throughout the entire region.
Other reports say no casualties or damage to property have been reported.
An earthquake of that strength is classified as minor but would be felt and might cause small damage to buildings.
Many South Africans in Gauteng province, which includes Johannesburg, said on social media they awoke to find the walls of their homes shaking.
Videos on social media showed the moment the quake struck.
Earthquakes are rare in South Africa. The last one to measure 5.0 magnitude or higher was in 2014, according to the US Geological Survey.
Below is a video compilation of the quake.
Meanwhile, Kanyi Daily reported that over 640 people were confirmed dead after a powerful earthquake hit Turkey and Syria.
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