The incident happened in KwaSobalili village, Ntabamhlophe, in Estcourt in the Midlands.
The little girl’s head was found by community members near the river on Saturday.
The suspect was arrested and is expected to appear in the Estcourt magistrate’s court this week.
“We condemn with the strongest terms possible such a barbaric act of this heartless criminal who murdered an innocent child.
“The gruesome circumstances of this case, where it is said that the child’s head was separated from the body, shows that the suspect had planned his act.