The soldiers will stay in Bujumbura until next June
Reports say the latest batch numbered about 240 troops, who join a first group of 240 who flew in from Pretoria on Sunday. Another batch is due to arrive on Saturday.
Under a deal brokered by former South African President Nelson Mandela, an interim government comprising both Hutus and Tutsis is to take power on Thursday.
The South African soldiers are tasked with guarding exiled Hutu leaders returning to participate in the transitional government.
Mr Mandela and as many as 10 African leaders are expected to attend the inauguration.
The main Hutu rebel groups are still refusing to take part in the transitional authority, and some hardline Tutsis are urging their supporters to attack the protection force.
Protection
South African Ministry of Defence spokesman Sam Mkhwanazi told the BBC that some 150 politicians would need to be provided with protection.
He said he had not heard of any reports so far of hostility towards the troops.
But a spokesman for a dissident wing of the Tutsi-dominated Union for National Progress said the South Africans had to be fought.
He told the AFP news agency they were "occupation troops sent here to protect people who committed genocide".
Mr Mkhwanazi said Pretoria was expecting the troops to be stationed in Burundi until June of next year.
UN support
The UN Security Council adopted a resolution on Monday in support of South Africa's decision to send troops to Burundi.
According to Mr Mkhwanazi, it is the type of peacekeeping operation that Pretoria hopes to repeat elsewhere on the continent.
"SA in general and the National Defence Force in particular is going to get more and more involved in peacekeeping missions of this nature," he said.
He did not elaborate on the countries where troops would deploy.
Burundi has been engulfed in civil war since 1993.
The conflict between the Tutsi-dominated government and the Hutu rebels has cost the lives of hundreds of thousands of people, and caused massive suffering.
Under the peace deal, Burundian President Pierre Buyoya, who is a Tutsi, will remain in office for 18 months before handing over to a Hutu.
The parliament in Bujumbura formally endorsed the plan on Tuesday whereby President Buyoya will by succeeded by his Hutu deputy, Ndayizeye Domitien.