Captain Kay Makhubela said Keketso Mahlakwana was found dead in a veld opposite Lenz Public Secondary School in Lenasia's Extension 6.
Makhubela said community members alerted police to the body.
Mahlakwana went missing outside Flamingo Primary School.
It was alleged that he was seen being dragged into a white taxi after school.
Makhubela could not confirm the cause of death, saying he was on his way to the scene.
Makhubela said police are investigating a case of murder. No arrests have been made.