The government's handling of the protests and violence has been criticised by other African nations, notably Ghana and Nigeria which are not in the SADC grouping.
President Cyril Ramaphosa closed a summit of the 16-nation Southern African Development Community (SADC) regional leaders with a request for joint efforts to tackle illegal migration to South Africa.
Weeks of protests by populist groups demanding undocumented foreign nationals go home by June 30 led more than 176,000 to flee in recent weeks, according to an AFP tally based on figures from the African governments involved.
"We thanked countries in our region for their understanding of the challenges that we faced and, in some respects, continue to face," the South African leader said in his concluding address in the coastal town of Durban.
"We also expressed regret at what has befallen us as a country. We expressed a wish that we should all work together to address the challenge of migration," he said.
Anti-migrant protesters at summit
The continent's wealthiest nation, South Africa has long been a draw for migrants but is battling an unemployment rate above 30 percent and massive inequality.
About 300 anti-migrant protesters marched on Monday to the summit venue, demanding the gathered leaders "fetch their people".
A helicopter and drones flew overhead as officers on horseback and motorbikes marshalled the relatively small group of marchers to the perimeter of the venue.
"We are here to tell you to come and fetch your people who are here in South Africa illegally," said march leader Jacinta Ngobese-Zuma, one of the figures behind the recent wave of protests.
She referenced Malawi, Mozambique and Zimbabwe, whose citizens made up the bulk of the thousands of foreign nationals who departed.
Discrimination and ill-treatment
Some left of their own accord but others were deported or helped out in government repatriation schemes.
Ramaphosa said at a public lecture Friday on the sidelines of the SADC meeting that South Africa was "deeply concerned and ashamed that nationals from other countries have in recent months been subjected to discrimination and ill-treatment".
At least four migrants were killed in the violence, according to the South African police, though some foreign governments say the toll is higher.
The government's handling of the protests and violence has been criticised by other African nations, notably Ghana and Nigeria which are not in the SADC grouping.
South Africa, which took over the rotating chairship of SADC at the summit, has called for an Africa-wide conference to address migration.
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