Police fired tear gas and rubber bullets to disperse the looters, while about 200 foreign nationals reportedly took refuge at a police station.
The attack came hours after thousands took part in a rally against xenophobia in the coastal city of Durban.
Anti-foreigner violence in recent weeks has killed at least five people.
Many jobless South Africans accuse foreigners of taking jobs in a country where the unemployment rate is 24%.
A crowd began looting foreign-owned shops in east Johannesburg on Thursday night, and a car, and a building believed to house foreigners, were set on fire.
The acting Premier of the Gauteng province around Johannesburg, Qedani Mahlangu, condemned the violence.
"We have to, each and every South African who's a peace-loving South African, to stand up and condemn this," she told the BBC.
"Today we can't... say that we want to live in isolation when the whole world is globalising."
On Friday, police dispersed a group of foreign nationals in Johannesburg who had armed themselves with machetes for protection, Reuters news agency reported.
The recent xenophobic attacks have also been condemned by President Jacob Zuma as "shocking".
"No amount of frustration or anger can justify the attacks on foreign nationals and the looting of their shops," he told parliament on Thursday.
Zulu King Goodwill Zwelithini has been accused of fuelling the attacks by saying that foreigners should "go back to their countries". However, he said that his comments had been distorted.
The police have established 24-hour joint operation centres to clamp down on attacks on foreign nationals, the BBC's Milton Nkosi in Johannesburg reports.
Many South Africans say they are embarrassed by the attacks on foreigners and hope they will end soon, our correspondent adds.
At least 62 people died in xenophobic attacks that swept South Africa in 2008.
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