Later, alleged anti-xenophobic protesters have attacked the offices of a South African company in Nigeria's capital Abuja, the Department of International Relations said.
Dirco spokesperson Clayson Monyela tweeted on Thursday: "A South African company offices attacked in Abuja #Nigeria a short while ago. Windows & several items broken..computers taken. Africa unite!"
There were unconfirmed reports that the offices belonged to MTN. The service provider could not be immediately reached for confirmation.
The Times reported that it was the MTN office that was attacked.
Earlier reports indicated that Nigerians staged an anti-xenophobia protest outside the South African embassy in Abuja on Wednesday, calling on authorities to "stop attacks on African nationals".
The protest, organised by members of the National Youth Council of Nigeria, urged the South African government to urgently address the situation.
The protesters carried placards such as "South Africa we say stop killing our people" and chanted slogans denouncing the attacks, the report said.
"We are doing this because of the killings taking place in South Africa, we want to express our displeasure over that and urge them to take measures to address the situation.
"We presented a petition in which we want them to call their people to order. We have foreigners here and it will not be good if there is reprisal attacks that will not make world a peaceful place to live," one of the protesters was quoted as saying.
Outbreaks of xenophobia violence were recently reported in Johannesburg and Pretoria.