Thousands of foreign nationals from elsewhere in Africa had already fled the country before Tuesday's "deadline" set by the demonstrators for all undocumented migrants to leave.
In parts of the main commercial city Johannesburg and the port city of Durban, hundreds of protesters marched swathed in South African flags and carrying wooden batons, watched by police with armoured vehicles and support helicopters.
Migrants have interpreted the deadline as a physical threat, and there were scattered signs of violence by midday, although marches were mostly peaceful.
Police said they had arrested some looters, giving no further details.
In Thembisa, a northern suburb of Johannesburg, rioters threw stones at police and suspected migrants, while sporadic gunfire could be heard near the central business district.
National paper the Daily Maverick reported police deploying tactical vehicles and firing shots in Benoni, eastern Johannesburg, after being threatened by 500 protesters.
In the densely populated township of Soweto, protesters looted some shacks of foreign nationals, national broadcaster SABC reported.
At least five people have been killed in violence since protests began in April, with thousands driven from their homes or seeing their businesses and property vandalised.
In such attacks, which have recurred sporadically in South Africa since 2008, little distinction is made between those who entered legally and those who did not.
The campaign group March and March, run by a former radio presenter behind the latest protests, denies encouraging violence, and says it cannot be held responsible for spontaneous acts of anger by South Africans towards undocumented migrants.
"We are trying to channel that anger towards the government," Jacinta Ngobese told Reuters in an interview two weeks ago.
"Unfortunately, we can't be in every single community telling them ... how to behave. They live with these people."
The marches in several cities were expected to draw many thousands of mostly poor or unemployed South Africans who blame foreign nationals for their hardships.
Thousands of police were deployed and military were on standby, a military spokesperson said.
The wave of anti-immigrant sentiment, and what critics say is a failure by police to protect victims, have tarnished South Africa's post-Nelson Mandela reputation as a defender of human rights and strained ties with other African nations.
Immigrants are blamed for taking jobs, driving crime and putting pressure on public services - claims that social scientists say lack evidence.
Thirty years since the end of apartheid, South Africa remains unequal, economic growth is slow and a third of people are out of work.
Despite this, it remains Africa's largest economy and continues to draw migrants.
The immigrant population stands at about three million or about four per cent of the total, according to StatsSA - a relatively low share by global standards.
