South African police have used rubber bullets, tear gas and water cannon to try and disperse anti-immigrant protesters in the capital, Pretoria.
A low-flying police helicopter has also been deployed amid a stand-off between local protesters and foreigners, with both groups armed with sticks, bricks and knives.
President Jacob Zuma had called for calm ahead of the anti-immigrant march.
Many unemployed South Africans accuse foreigners of taking their jobs.
Mr Zuma has condemned the acts of violence and intimidation directed at African immigrants living in South Africa.
Earlier this week, angry mobs attacked Nigerians and looted shops belonging to Somalis, Pakistani and other migrants in townships around Pretoria and parts of Johannesburg.
The main group behind the Pretoria protests, Mamelodi Concerned Residents, has blamed foreign nationals for taking jobs and accused them of being involved in prostitution rings and drug cartels, accusations denied by immigrant communities.
The petition delivered by the group to the home affairs ministry alleged worshippers from Zimbabwean apostolic churches, who congregate in the open, were “destroying our public parks”, and accused them of defecating, urinating and burning fires.
It also said foreigners were “arrogant and don’t know how to talk to people, especially Nigerians”.
But President Zuma said many foreign citizens living in South Africa were law-abiding and contributed to the economy.
“It is wrong to brandish all non-nationals as drug dealers or human traffickers. Let us isolate those who commit such crimes and work with government to have them arrested, without stereotyping and causing harm to innocent people,” Mr Zuma said in a statement.
He said he would be championing the fight against crime to promote safer and more stable communities.
The home affairs minister announced plans on Thursday to inspect workplaces to see if firms are employing undocumented foreigners.
Police in Pretoria say they have made more than a hundred arrests in the past 24 hours, amid the unrest.
In a statement, they blamed a group from the Atteridgeville township in Pretoria, who were not part of the sanctioned protest, for this morning’s violence.
The foundation of late South African leader Nelson Mandela says it was shocked at the decision by police to give the go-ahead for Friday’s anti-foreigner protest, calling it “a march of hatred”.
Official government figures say the number of immigrants in South Africa has declined in recent years.
Figures released last year said there were 1.6 million foreign-born people in the country, down from 2.2 million in 2011.
South Africa experienced its worst outbreak of violence against foreigners in 2008, when more than 60 people died.
Two years ago, similar xenophobic unrest in the cities of Johannesburg and Durban claimed seven lives as African immigrants were hunted down and attacked by gangs.