In the latest of periodic xenophobic violence in South Africa, deadly riots last week in Pretoria and Johannesburg killed at least 10 people including two foreigners, and targeted foreign-owned businesses.
South Africa has faced widespread criticism for its latest outbreak of xenophobia or "Afrophobia" attacks as official responses included Nigeria boycotting the World Economic Forum Africa hosted in Cape Town last week, while Zambia and Madagascar also cancelled planned soccer games with South Africa's national team.
The flare-up in violence directed against mainly African foreigners has been widely condemned by South Africa's neighbours and has caused a diplomatic dispute between Nigeria and South Africa, the continent's top two economies.
Nigerians have gathered round the consulate in South Africa for departure, although invalid papers appear to be slowing down the process.
Al Jazeera's Fahmida Miller reports from Johannesburg, South Africa.
A riot police officer throws a teargas canister as looters make off with goods from a store in Germiston, east of Johannesburg on September 3. Logistics for the evacuation will be provided by Air Peace, a Nigerian airline which has offered to airlift Nigerians.
He thanked the Nigerian government and the High Commission in South Africa for their assistance. The police confirmed 12 people have been killed and 639 people had been arrested as of Monday after the latest wave of attacks as dozens of foreign-owned businesses are looted and destroyed.
Commercial Nigerian airline, Air Peace, says it plans to operate two flights with Boeing 777 aircraft for the job of evacuating as many Nigerians as possible.
"The ANC will also use the opportunity to clarify the parties on the recent acts of violence in South Africa which have largely been labelled by the media as xenophobic attacks", ANC national spokesperson Pule Mabe said.