Springs police spokesman Captain Johannes Ramphora says the child was last seen at around 3.30pm on Tuesday and was reported missing around 8pm.
He says according to the mother of the child, she had an argument with her boyfriend who she alleges threatened to kill her and the boy before he disappeared.
The police were called to the scene by a homeless man who alleges to have heard a loud sound at around 8pm on Tuesday.
He says when the police arrived on the scene, they found a container of tablets which was sent to forensics.
A case of murder has been opened and is being investigated.
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