Mbeki has been criticised for reacting slowly when mobs rioted in townships around Johannesburg and other cities for two weeks in May, beating foreigners and looting and burning their properties. Sixty-two people died and tens of thousands fled.
The bloodshed stoked fears of political instability in Africa's richest economy at a time when it was moving ahead with preparations to host the 2010 soccer World Cup. An estimated 500,000 foreign visitors are expected for the tournament.
"I will not hesitate to assert that my people are not diseased by the terrible affliction of xenophobia ...," Mbeki said in Pretoria during a candlelit remembrance for the victims and their families.
"The dark days of May, which have brought us here today, were visited on our country by people who acted with criminal intent," Mbeki said. He also apologised to immigrants on behalf of his government and the country.
The attacks, which only ended after the army was deployed, were an embarrassment to Mbeki's government. It has opened the doors to millions of African migrant workers and refugees and made African unity a cornerstone of its foreign policy.
The South African leader's explanation, however, did not ring true with some of those who attended the ceremony.
"What he is saying on that podium is not what I am seeing on the ground," said Clement Sakala, a 50-year-old Zimbabwean refugee whose family was attacked in an informal settlement near Pretoria during the violence. "I still can't go home."
An estimated three million Zimbabweans live in South Africa, which has a population of about 47 million people. The Zimbabweans, most of whom have fled an economic crisis at home, are accused of stealing jobs and fueling high levels of crime.
Tensions between native-born South Africans and immigrants have risen due to growing competition for housing and jobs and the impact of soaring food and fuel prices. Unemployment in South Africa hovers around 24 percent.
The situation has been exacerbated by rising anger over the government's failure to provide electricity, sewage facilities and other basic services to many poor residents.
"It is wishful thinking to say it is just criminality that caused this," said Susan Booysen, a political analyst at South Africa's University of the Witwatersrand. "It is a compilation of some crime, xenophobia and non-delivery (of services)."
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