The row strained ties between two African states involved in efforts to bring peace to eastern Democratic Republic of Congo, where South Africa has troops in a United Nations (UN) brigade that fought last year against rebels whom UN experts said received support from Rwanda. Kigali denied backing the Congolese rebels.
Late on Monday, armed men broke into the Johannesburg home of former Rwandan army chief General Faustin Kayumba Nyamwasa, an exiled critic of Rwandan President Paul Kagame.
Nyamwasa, who survived an assassination attempt in Johannesburg in 2010, was not in the house at the time.
A diplomatic source, who asked not to be named, told Reuters that South African security services had tracked the attackers. "It was very clear that they were intelligence personnel attached to the Rwandan embassy," the source added.
Three diplomats from the Rwandan mission in Pretoria were ordered out of the country in 48 hours this week. Kigali's tit-for-tat expulsions followed on Friday.
"We have expelled six South African diplomats in reciprocity and concern at South Africa's harbouring of dissidents responsible for terrorist attacks in Rwanda," Rwandan Foreign Minister Louise Mushikiwabo said in a comment on her Twitter account.
South African police have also been investigating the New Year's Eve murder in a posh Johannesburg hotel of another exiled Kagame opponent, former Rwandan spy chief Patrick Karegeya.
Exiled Rwandan opposition members have accused Kagame and his government of being responsible for Karegeya's death and for attacks on Nyamwasa and other overseas-based critics.
They deny Kigali's charges that they are behind "terrorist" attacks in Rwanda.
Kagame and senior Rwandan officials have denied any involvement in the attacks on exiled opponents but have called them traitors who should not expect forgiveness or pity.
Brian Dube, spokesperson for the State Security Agency, would not comment on the expulsions but confirmed the country's security services had been looking into the attacks against the exiled Rwandans.
The US in January expressed concern over what it called "politically-motivated murders of prominent Rwandan exiles".
David Batenga, a nephew of the slain Rwandan spy chief Karegeya, called for the closure of the Rwandan embassy in South Africa.
"It's not an embassy, it's an operation centre for planning missions to kill innocent civilians," he told Reuters.
Etienne Mutabazi, deputy chairperson in South Africa of the opposition Rwanda National Congress, of which Karegeya and Nyamwasa were founding members, said the expulsion of the Rwandan diplomats was "long overdue" and called their activities "criminal".
"Diplomats are here to represent their country, they have immunity but they should not abuse that immunity," he said.
In January, Kagame, who has won Western praise for rebuilding Rwanda after the 1994 genocide there, defended his nation's right to self-defence against those who "betray" it.
"We didn't do it, but my question is – shouldn't we have done it?" Kagame said at a January 12 prayer breakfast, clearly referring to Karegeya's death but without naming him.
"No one will betray Rwanda and get away with it. Regardless of who you are, there will be consequences," Kagame said.
Karegeya fled to South Africa in 2007 after allegedly plotting a coup against Kagame with Nyamwasa. – Reuters