Kigali expelled eight South African diplomats, after Pretoria gave three Rwandan officials 72 hours to leave the country, diplomatic sources said.
The Rwandans are suspected of being linked to an assassination attempt on the Johannesburg-based former Rwandan army boss Faustin Kayumba Nyamwasa.
A group of armed men raided Nyamwasa's house in the city's southeast overnight Monday to Tuesday "looking for him" the opposition Rwanda National Congress said.
Nyamwasa has already survived two assassination attempts.
The party "has no doubt that those who have always attempted to get rid of General Nyamwasa may also be behind the attack."
More From This Section
South African foreign affairs officials refused to comment saying a statement would be issued later.
South Africa is home to numerous Rwandan dissidents, a point of bitter dispute between the two countries.
Tensions deepened after Kigali's former intelligence chief Patrick Karegeya, who was also exiled in South Africa, was found strangled to death in a Johannesburg luxury hotel on New Year's Day.
Some opposition members charged the Rwandan government was behind the attack.