The Department of Transport said on Thursday (March 28) that at least 45 people had been killed.
The driver lost control and collided with barriers on a bridge near Mamatlakala.
The bus went over the bridge and hit the ground, catching fire, according to the transport department.
It added that the bus was taking Easter pilgrims from Botswana to Moria, a town in Limpopo.
South African President Cyril Ramaphosa sent his condolences to Botswana and pledged support to the country, his office said in a statement.
Limpopo's Department of Transport said only an eight year-old survived the crash and was receiving medical attention at a nearby hospital.
Some bodies were burned beyond recognition while others were trapped inside the debris or scattered on the scene, the provincial department said.
