The warning comes as low-lying areas in the city experienced flooding and cars were submerged in Benoni and surrounding areas, including Lakefield and Van Dykpark in Boksburg.
Forecaster Lehlohonolo Thobela told said the heavy rains affected most parts of the East Rand, with Benoni and Boksburg being the hardest hit.
He said there would be a 30% chance of rainfall in several parts of the country and Gauteng throughout the weekend. He said although this is lower than the current rainfall, areas already submerged in water would be at risk of further flooding.
On Thursday, SAWS issued a yellow level 2 weather warning for Gauteng. It said the heavy rains would be concentrated in Ekurhuleni and Tshwane. It said the warning implied a high likelihood of minor impact, meaning there would be isolated flooding incidents.
Emergency services spokesperson William Ntladi said that most areas were affected by heavy rains in the East Rand. He said they remained on high alert but had not received reports of deaths or damage to infrastructure.
Safety tips include avoid low-lying routes for motorists and pedestrians, adhering to warnings issued by local municipalities and avoiding speeding while driving.