The Ministry of Police said the protests had largely been peaceful across the country, with isolated incidents of looting.
However Police Minister Firoz Cachalia confirmed that the army was deployed “on a contingency basis” in parts of Johannesburg as well as Durban.
Police also confirmed the arrest of three people in Hillbrow, a suburb in Johannesburg with a high migrant population, after two people were injured during protests.
According to police, the trio “opened fire at protesters who were passing through the street” and the marchers retaliated by “torching the suspects’ vehicle”. Among the injured was a 17-year-old.
Some protesters threw bricks, breaking the windows of some homes in Yeoville, another suburb where many African migrants live.
Shops in the city centre were closed, while police visibility is high on major streets.
In a neighbourhood in Germiston, about 15km (nine miles) from Johannesburg, demonstrators went to homes, evicting residents they suspected were foreign nationals and handing them over to police officers, insisting they check their documentation, local media report.
Police said they had arrested five people for the alleged looting of a foreign-owned shop in Johannesburg’s biggest township, Soweto.
About 10 people were also arrested for looting in KwaZulu-Natal province, while a woman was arrested for assaulting a police officer and a man for “intimidation” following reports of a foreign national being beaten up, police said.
Businesses in central Durban, the main city in the province, were also shut.
Protesters handed over a memorandum listing their demands to government officials in Durban and Johannesburg.
The leader of anti-migrant group March and March, Jacinta Ngobese-Zuma, said they would protest every Thursday for the next six months to force the government to “get rid of” undocumented migrants who were still in South Africa.
A demonstrator – who is part of another anti-migrant group, Operation Dudula – told the BBC they would “push the police” to arrest foreigners who are not legally in the country.
President Cyril Ramaphosa met some of the protest leaders on the eve of Tuesday’s marches to defuse tensions.
He has repeatedly warned demonstrators to act peacefully, while also accepting the need for immigration reforms.
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