The talks would be hosted by South African Deputy President Jacob Zuma, his office said.
Spokeswoman Lakela Kaunda said FNL rebels led by Agathon Rwasa, who has refused to strike a ceasefire deal with Buyoya, would not be present.
"They will have to be engaged at some (other) point," Kaunda said.
The groundwork for sending an African peacekeeping force to reinforce the peace efforts in strife-torn Burundi would also be discussed.
Buyoya was expected to arrive in Pretoria on Friday.
On Saturday, he would hold talks with the rebel leaders who signed a ceasefire accord with the Bujumbura government in October last year.
They are Jean-Bosco Ndayikengurukiye and Alain Mugabarabona, who respectively head splinter groups of the Hutu rebel Forces for the Defence of Democracy (FDD) and the National Liberation Forces (FNL).
The two are believed to command insignificant numbers of militia in the Burundi civil war that has claimed more than 300000 lives since October 1993.
Kaunda said Buyoya would meet Pierre Nkurunziza, leader the main FDD rebel group, on Sunday.
The two leaders signed a ceasefire agreement early in December, raising hopes that a peaceful settlement in Burundi might be within reach.
Maintaining the truce, however, has already proved to be difficult.
Burundi's army claims it has problems distinguishing FDD rebels from fighters refusing to lay down arms.
For its part, the FDD, has accused the army of reckless and indiscriminate shelling.
Under the ceasefire agreement, FDD cadres and government troops were to have stopped shooting at each other within 72 hours of the signing of the ceasefire on December 3.
It is hoped that the deployment of an African peacekeeping force - to be drawn from the defence forces of South Africa, Mozambique and Ethiopia -will help cement the ceasefire.
The first talks on details of putting such a force together were held in Pretoria on Tuesday between the defence ministers of South Africa and Mozambique.
Kaunda said on Thursday: "The Deputy President looks forward to the weekend meetings, as they will assist in speeding up the implementation process and in advancing preparations for ... the deployment of the African Mission force in Burundi."
Zuma had already discussed some aspects of the ceasefire agreement with Ndayikengurukiye and Mugabarabona, in Pretoria on Tuesday night.
These included the return of former fighters and leaders to Burundi and the participation of former armed movements in transitional state institutions.
The two rebel leaders, who are currently in exile, told Zuma they would return to Bujumbura in two weeks' time, Kaunda said - Sapa
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