Michaela Williams was last seen at her Grassy Park home on Tuesday afternoon, according to Col Andrè Traut. Her mother contacted police in the early hours of Wednesday.
Traut said Michaela was last seen in the company of a man who lived in the same street.
On Thursday, Brig Novela Potelwa said: “Vital information was followed as part of the investigation and the suspect interviewed. The interview led to him pointing out where the body was. The suspect has been charged with murder.”
Michaela’s remains were found in Philippi.
A postmortem will be conducted to determine how she died.
The suspect is expected to appear in the Wynberg magistrate’s court on Friday.