President Jacob Zuma was thronged during a walkabout in Marabastad‚ west of Pretoria‚ on Monday. .
The face of Neo Ramaswe, 13, was skinned and his throat, tongue and kidneys were removed, possibly for making muti, said Captain Amanda Funani.
Muti is traditional African medicine.
Ramaswe's body was found on Sunday in an open field by a passer-by in the area, but police only disclosed the information to media on Wednesday.
"He was last seen by his friends [last Thursday]... after playing soccer," said Funani.
Police have launched a manhunt for two men suspected of involvement in his death, after they were seen talking to him.
A case of murder has been opened.