The medium-sized mining company DRDGold said two of its workers killed on Tuesday - one of whom was South African - had died in violence in the Ramaphosa township near Johannesburg.
The workers were from the East Rand proprietary mine where the company said more than half of the miners on Thursday's day shift had failed to report for work. Almost a third of the mine's semi-skilled workers are foreign.
Miners' union officials have been discussing the disruption with representatives of the Mozambican workforce.
Meanwhile, Mozambique has provided buses to take about 9,000 people home.
The BBC's Karen Allen saw chaotic scenes and scuffles at a Johannesburg police station, as Mozambicans tried to scramble on board buses to take them home.
Leonardo Boby, deputy national director of migration, said about 3,000 people had returned to Mozambique each day this week.
The makeshift camps where displaced foreigners seek shelter
Some Zimbabweans are also going home, preferring to risk the violence there than stay in South Africa.
One Zimbabwean woman told the BBC she had decided to return home from Johannesburg after seeing a series of xenophobic attacks.
The 36-year-old woman said she had seen an armed gang douse a Mozambican immigrant with petrol and throw him into his burning shack.
"The screams of the burning Mozambican still haunt me. When I close my eyes to try to sleep, I see the man screaming for help. But no-one helps him," she said.
"I have never seen such barbarism."
The director general of South Africa's National Intelligence Agency, Manala Manzini, said on Thursday that the attacks were unleashed by movements that supported the apartheid government.
The unnamed groups had delivered weapons to hostels in the townships, he said.
Correspondents say he is believed to be referring to the Inkatha Freedom Party, whose members are mainly Zulus. It has denied any role in the violence.
Mr Manzini's comments were echoed by the minister of intelligence, Ronnie Kasrils, who said there were groups that had what he called their own political agenda.
"There was organisation... we have names of people who called meetings," he said.
The secretary general of the ruling African National Congress (ANC), Kgalema Motlanthe, has said that many of the immigrants were able to get jobs in South Africa because they were better qualified than locals, whose education was disrupted by apartheid.
He said this was a cause of envy from South Africans, who needed to acquire the skills that would enable them to make a living.
The violence began on 11 May in a township north of Johannesburg, before spreading to the city and the surrounding region.
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