Police officers were combing a dumping site in Bloekombos for clues on Thursday morning after the body of nine-year-old Previledge Mabvongwe was found there.
The girl's body was discovered around 08:40, said Western Cape police spokesperson Sergeant Noloyiso Rwexana.
"The deceased was still dressed in her school uniform when her body was found at a dumping site in Sam Jokozela, Bloekombos."
Mabvongwe went missing on Monday afternoon after she was dropped off by a taxi close to her home.
She had been wearing her blue school jersey, navy school skirt and black shoes at the time.
Rwexana said crime scene experts and members of the Kraaifontein family violence, child protection and sexual offences team were on the scene.
Cases of murder and abduction had been opened for investigation.
The discovery comes just days after Western Cape Education MEC Debbie Schafer warned parents and children about the risk of abductions, after hearing about three incidents in Cape Town.
She said her department had received reports of two kidnappings in the Zonnebloem area and an attempted abduction in Rylands earlier this month.
'Stranger danger'
Schafer confirmed that a Grade 9 pupil from a southern suburbs school had been abducted and allegedly sexually assaulted while on her way to school on August 23.
"The learner reported that men in a white BMW with tinted windows stopped next to her and pulled her into the car, before driving around with her for hours," she said.
The matter had been reported to Steenberg police and the learner had received medical attention. A school social worker and psychologist were also providing counselling to the learner and her family.
Rwexana said that a case of rape had been opened.
Schafer said that pupils who had to walk to their public transport departure points should travel in groups at all times.
"However, where feasible, parents must please arrange that this is as close to the school as possible."
Schools should ensure that learners were aware of "stranger danger", as children "must know that they should be wary and immediately seek help if a stranger approaches them".
Anyone with information on the Mabvongwe case can contact investigating officer Captain Loganathan Chetty on 082 522 1039.