Mojapelo said the man had fetched his son from the mother, who is staying in Gauteng, two weeks earlier.
"The community members saw the suspicious grave and questioned the suspect, who tried to run away but was traced and arrested. The suspect was admitted in hospital with serious injuries and is under police guard," he said.
In a video clip that has emerged, the man, wearing a green T-shirt and blue trousers, is seen surrounded by angry community members demanding the boy's body. He is seen using a spade to dig up the shallow grave. When he reaches the body, it is in a mealie-meal bag covered in a blanket.
One of the community members can be heard saying that the man confessed to killing his son and burying him in a shallow grave in the backyard.
"He said he didn't know what got into him when he killed his son," he said.
Another resident can be heard saying that the body was scalded with boiling water.
"We can confirm that the case of murder has been opened and the father will appear in court soon," added Mojapelo.