Local media reported that Gwadiso had been asked to return "for consultations over the issues in that country".
Relations between the two nations have been strained since June, when General Faustin Kayumba Nyamwasa, a critic of the Rwandan president Paul Kagame, was shot in the stomach in Johannesburg. He had fled Rwanda four months earlier.
Nyamwasa survived but insists that the attack was an assassination attempt. Authorities have arrested five men over the shooting, revealing their nationalities.
Rwandan authorities have denied any involvement in the incident and demanded that Nyamwasa be extradited to their country.
In July, Rwanda summoned Gwadiso to express concern about the South African investigation.
"We are not making any connections by recalling our ambassador. We are also not making any connection between the government of Rwanda and the shooting of the general," Ntsaluba said.
Rwanda is to hold presidential elections on August 9. The build-up to the polls has been blighted by violence and accusations that the opposition has been marginalised by the incumbent government.
Opposition groups have said that more than 30 newspapers have been banned in recent months and Amnesty International has said that there is a climate of repression.
Tawanda Hondora, the Africa deputy programme director of Amnesty International, told Al Jazeera: "Opposition party figures have been intimidated. Journalists have been targeted and killed, and army generals critical of the ruling party attacked and arrested.
"That environment would clearly create fear ... and very little has been done to ensure that anyone will be brought to justice ... It is a police state."
Louise Mushikiwabo, Rwanda's foreign minister, refuted the claims.
"The international media and human rights groups are misrepresenting what is happening in the country," Mushikiwabo told Al Jazeera.
"My government does not stand to gain from any actions of insecurity. Paul Kagame happens to be a very popular candidate. I think to point a finger at this government is wrong.
"Anyone who is reading the situation from Rwanda would know that there is an atmosphere of excitement among the public."