The suspects were found just after midnight yesterday hiding in a cave on a mountain near the village.
Limpopo police spokesperson Brigadier Hangwane Mulaudzi said police launched a massive manhunt after a tip-off from members of the community, who told them the whereabouts of the suspects.
He said the police went to the houses of the suspects at about midnight.
"We arranged a helicopter and at about 4am, we managed to locate our first suspect, who led us to the others." Mulaudzi said.
He said the suspects would appear in the Naphuno magistrate's court tomorrow for attempted murder and two counts of murder.
The arrest was a sequel to an incident that took place on Monday at Bokgaga village when a group of people assaulted, stoned to death and burnt an 81-year-old grandmother and a 26-year-old woman.
It is alleged the group accused the victims of practising witchcraft.