Inspector Aubrey Moopeloa said the incident happened on Saturday afternoon.
"Apparently they were playing and the 13 year-old took him to a kraal."
The rape then allegedly took place, he said.
In a separate incident, two men aged 28 and 30 were arrested following the rape of a 22-year-old woman, said Moopeloa.
The woman was apparently attending a party on Friday night when she asked one of the men to accompany her home so she could get her jersey.
The man allegedly came along with a friend and they took the woman to another house instead.
One of the men raped her but police managed to get to the house early on Saturday morning before the second man could rape her.
Moopeloa said party-goers called police on realising that the woman had not returned to the party.
Meanwhile, 171 other people were arrested in the township during the weekend for crimes including arson, theft and assault.
A video of a boy being forced by his parents to run almost naked in the snow has sparked an uproar.
Cosatu met with the Public Protector to discuss its numerous complaints against Premier Helen Zille.
Marine ruins have been discovered by builders working at the V&A Waterfront in Cape Town.
