Zwelithini had made an angry speech last month blaming immigrants for rising crime and saying they must leave the country, in an outburst seen as encouraging the spate of attacks on Zimbabweans, Somalians, Malawians and other foreigners.
But he told a tribal gathering of several thousand Zulus in the port city of Durban that he had been misrepresented.
"My speech... was directed at the police, calling for stricter law enforcement, but that was never reported," he said.
"The public was instead given another side of my speech, which had been twisted and misrepresented.
"This violence directed at our brothers and sister is shameful."
South African authorities have struggled to contain mobs in the economic capital Johannesburg and Durban who were hunting down foreigners.
At least seven people have been killed and 307 suspects arrested in the worst ethnic violence since 2008, when 62 people were killed mainly in Johannesburg's townships.
Numbering 12 million people, the Zulus are the largest ethnic group in South Africa and Zwelithini, their traditional leader, retains great influence over his subjects.
Wearing a suit and tie rather than his royal animal-skin dress, he told the audience that he had never called on his people to attack foreigners.
"Had I said that, this country would be in ashes," he said to loud cheers.
Many in the stadium, which was built for 2010 football World Cup, booed when foreign dignitaries were introduced and during multi-faith prayers.
Violence has fallen in recent days in Johannesburg and Durban, but the rioting and looting have exposed deep tensions between South Africans and immigrants from across the continent.
Immigrants are often the focus for anger among locals hit by a chronic job shortage and the limited progress made by many poor blacks since white-minority rule ended in 1994.
President Jacob Zuma has moved to counter claims he was ignoring the attacks, which provoked outrage from neighbouring countries whose citizens have been targeted.
"Millions of South Africans condemn these atrocious killings and abhor xenophobia and all related intolerances," he said in a statement released on Monday.
"Together we must work harder to root out violence and hatred in our society."
Several thousand immigrants have been forced from their homes and are staying in camps, while Zimbabwe, Malawi and Mozambique have organised for some worried citizens to return home.