A passerby discovered the bodies - buried in a single shallow grave - behind Slovoville cemetery in Soweto.
They had been blindfolded and their hands were tied, police spokesperson Captain Kay Makhubele told News24 at the time.
On Wednesday, Makhubele told News24 that the boy, 10, and girl, 11, were brother and sister.
The mother's boyfriend is the main suspect in the disappearance and murder of the two children, Makhubele told News24.
The suspect has, however, not been arrested or taken in for questioning, and was still being sought by police.
"In line with the national instruction to prioritise cases against women and children, police will leave no stone unturned to ensure that the perpetrators of this heinous crime against the children are found [and] face the full might of the law," Makhubele said.