A 27-year-old man was allegedly stoned to death by a couple in Ekurhuleni after he was mistaken for an intruder.

According to Putfontein police, the couple was arrested and has been charged with the murder of Lebogang Mashala, who "gate-crashed" their yard on Sunday.

Constable Justice Ramaube said the male suspect has since confessed to killing Mashala, claiming he mistook him for an intruder.

"The suspect said when he found Mashala in his yard at 3am and asked him what he was doing, a fight broke out. The suspect confessed to attacking Mashala with his girlfriend by stoning him with bricks," Ramaube said.

"The suspect said Mashala was overpowering him during their fight; he then decided to defend himself using the bricks in his yard."

Ramaube said the couple repeatedly stoned Mashala on his head as he lay on the ground. He said Mashala had a big gush on his head where he had been hit repeatedly.

Mduduzi Khumalo, a neighbour who passed by the scene where Mashala lay dead after the attack, said he was called by the suspect while walking past his gate to call the police.

"I then walked closer to see what was going on... I noticed a man lying by the locked gate in a pool of blood and I immediately woke up neighbours for help," said Khumalo.

He said when neighbours arrived they blew a whistle to wake up the rest of the neighbourhood.

"They asked the man to open the gate so they can question him [but] he ran to the back of his shack and vanished. He was later found lying flat on his stomach on top of a shack that is opposite to his."

Khumalo said angry community members said they did not believe he killed Mashala for being an intruder

Another neighbour, Lerato Mabaso, said when police arrived the community had started attacking the suspect who allegedly killed Mashala.

When Sowetan visited Mashala's family, a man who identified himself as his uncle, said the family was not ready to talk about the killing.

Ramaube said the motive for the killing was still unclear.