Homes and shops of Nigerians have been targeted and looted in Pretoria West in recent days.
Buildings with Nigerian businesses have been burned in Johannesburg’s Rosettenville suburbs in the past few weeks.
Nigerian Foreign Minister Geoffrey Onyeama said his ministry had summoned the South African ambassador to discuss the matter.
The incident is the latest development in the rivalry between the countries with Africa’s two largest economies.
Relations have been strained by accusations of South African xenophobia, with Nigerians alleging that Pretoria subjects them to harsh visa restrictions.
In the streets of Abuja, Nigerians expressed their anger over the attacks.