Protests were held outside the consulate and at the South African High Commission in Abuja.
South African consul general in Nigeria, Sam Monaisa, said in an email to the South African business forum in that country that the closure would remain in force until Thursday.
The situation in Durban had calmed down, but he was concerned about the Nigerians that were being repatriated, he wrote.
He said Nigerians were using social media to blow an already tense situation in South Africa out of proportion and stoking emotions.
This was why Nigerians maintained that their compatriots were being killed daily in South Africa, he said.
South Africans becoming targets
He warned the forum’s members to stay alert and not move around unnecessarily. South African businesses and citizens became targets of threats and acts of retaliation whenever xenophobic attacks occurred in South Africa, he cautioned.
Meanwhile, in Zimbabwe 15 people who were part of a first group of Zimbabweans returning home in the wake of xenophobic attacks in Durban have “disappeared” in Musina, state media reported on Tuesday.
The Herald newspaper said in an online update: “Fifteen victims disappeared in Musina where they reportedly claimed feeling safe because there were no xenophobic attacks reported.” There were no further details.
Zimbabwe is repatriating up to 2000 of its citizens who have asked to be evacuated in the wake of the attacks.
The first six buses carrying 407 Zimbabweans left Durban on Sunday.