The men were killed yesterday night during a raid on a shop owned by a Somali immigrant in central Johannesburg.
"During the commotion, shots were fired and two males were killed," said police spokesman Lieutenant-General Solomon Makgale. "It appears that the looters fired the shots."
The violence began a week ago in the township of Soweto -- once home to two of South Africa's Nobel laureates, former president Nelson Mandela and Archbishop Desmond Tutu -- after a foreign businessman shot dead a local teenager who had allegedly tried to rob him.
On Friday, a 13-month-old baby was trampled to death when it fell from its mother's arms in the middle of a looting spree, police said.
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The deaths bring the total number of deaths linked to the violence to at least six.
In the latest violence, an engineering firm next to the Somali shop was set alight last night, while another two shops in the northern Johannesburg township of Alexandra were targeted early today.
Ten foreigners, meanwhile, face gun charges after being found with unlicensed firearms.
Other foreigners have fled the townships to immigrant-friendly suburbs to escape the violence that they describe as xenophobic.
Police have insisted the looting is opportunistic criminality.
The violence has been condemned by rights groups and politicians, with President Jacob Zuma urging the police to restore order.
Foreign-owned businesses have cropped up in most South African townships, and locals often accuse the foreigners of putting them out of business with low prices.