The South African embassy in Lagos, Nigeria, was forced to close its doors on Wednesday after it came under attack, EWN and eNCA reported.
The Department of International Relations and Cooperation (Dirco) reportedly said it was assessing the damage. It was reported that a vehicle was vandalised during demonstrations.
Some South African businesses operating in Nigeria, including MTN, have reportedly closed until further notice after being attacked.
The announcement, which signals worsening diplomatic relations between the two African countries, comes after Nigeria introduced plans to evacuate its nationals in South Africa following a wave of attacks on foreigners, including Nigerians.
It also came a day after Nigeria pulled out of the World Economic Forum (WEF) gathering in Cape Town, casting a cloud over initiatives to boost intra-African trade.
Nigeria also recalled its High Commissioner to South Africa, Ambassador Kabiru Bala.
Violence across Gauteng resulted in seven confirmed deaths and more than 180 arrests as police and residents clashed, News24 reported. Several areas in the province were plagued by violent protests and looting since Sunday.
Nigerian President Muhammadu Buhari's government summoned South Africa's envoy to the World Economic Forum (WEF) on Tuesday and said it would dispatch a delegation to Pretoria to express "deep concern" over attacks on Nigerians, AFP reported.
Buhari "has noted with deep concern, reported attacks on Nigerian citizens and property in South Africa since August 29, 2019", his presidency said in a statement.
President @MBuhari and the government of Nigeria expect all Nigerians to stand on a high moral grounds.— Lauretta Onochie (@Laurestar) September 4, 2019
We cannot be seen to be doing what we condemn in South Africa by vandalising Businesses linked to South Africa in Nigeria.
We are the victims. Lets not be the oppressors too pic.twitter.com/WsLn4Xb6Dj
The president ordered the foreign minister to summon the South African envoy for a brief on the situation, to express Nigeria's displeasure and to get guarantees for the safety of its citizens and their property.
A special envoy from Buhari was due to arrive in Pretoria on Thursday to convey his displeasure to President Cyril Ramaphosa.
A Nigerian government spokesperson said on Wednesday night that Buhari was "distraught at the acts of vandalism that have taken place here in Nigeria in retaliation to what is happening in South Africa. We have to take the moral higher ground."
Lauretta Onochie, an aide to Buhari, tweeted on Wednesday: "We cannot be seen to be doing what we condemn in South Africa by vandalising Businesses linked to South Africa in Nigeria. We are the victims. Lets not be the oppressors too. (sic)"
Dirco's Lunga Ngqengelele told EWN: "There were some people who attacked the embassy. We are still trying to verify the information in terms of the damage that might have occurred. Fortunately, no one has been injured."
- Compiled by Riaan Grobler