SANDF soldiers were deployed on Tuesday to try to quell the unrest after being criticised by governments including China and Zimbabwe for failing to protect foreigners from armed mobs.
"The essence of the summon was to register Nigeria's protest over the on-going xenophobic attacks against fellow Africans in South Africa," the ministry said, adding that the meeting had happened on Monday.
It also called on authorities to quell the unrest and bring those involved to book.
On Tuesday, four men aged between 18 and 22 were charged with the murder and robbery of a Mozambican man, Emmanuel Sithole, whose death was captured by a newspaper photographer and plastered across the front pages, shocking the nation.
Isolated counter-protests involving a few dozen people have occurred in Nigeria, an economy in which South African firms such as mobile phone giant MTN and supermarket chain Shoprite have large stakes.
Diplomats from several African countries have urged their citizens back home not to seek vengeance.
"We are appealing to our countries not to retaliate," Democratic Republic of the Congo Ambassador Bene M'Poko told a news conference in Johannesburg, stressing that South African firms in the rest of the continent were "working peacefully".