Johannesburg — South African Prime Minister Pieter W. Botha has done the unthinkable: He has fractured the political unity of the Afrikaners, expelling 16 fellow Nationalists from his party.
The break is the deepest split since the National Party gained power in 1948 and ushered in South Africa's apartheid system.
The prime minister, freed of his vocal right wing, could now move ahead more boldly with liberal internal reforms.
Mr. Botha also gains a freer hand in resolving the nagging problem of Namibia (South-West Africa). A pervasive belief is that Pretoria is reluctant to yield the mineral-rich territory because it might produce a white backlash in South Africa.
Far from being a personal and political disaster, the split in the ranks of the ruling National Party so far appears to have been a boost to Mr. Botha's leadership. It has:
* Established clearly Mr. Botha's firm control and authority over South Africa's ruling National Party.
* Gained the prime minister some political support beyond the conventional boundaries of his own party. A number of political opponents have branded his action ''courageous.''
* Arrested, momentarily at least, mounting cynicism about his commitment to ''reformist'' racial policies for South Africa.
* Given Mr. Botha a ''window of opportunity'' in the near term to pursue more freely his own, still largely undefined, agenda of ''reform.''
''Nationalist prime ministers have been mesmerized by the need for unity of the Afrikaner party (National Party). Now (Mr. Botha) has set himself free of this preoccupation,'' says Bishop Desmond Tutu of the South African Council of Churches.
What Mr. Botha does from his position of enhanced strength remains to be seen. Opponents have long felt the prime minister has overestimated the strength of the right-wing threat, and some fear he will continue to do so.
In splitting off the right wing of his own party over the issue of limited ''power sharing,'' Mr. Botha has provided seed for more formidable far-right electoral opposition to the National Party than now exists.
But this opposition is generally regarded as more of a long-term threat than an immediate one. Dr. Andries Treurnicht and the other Nationalists in Parliament who opposed and eventually lost their power struggle with Mr. Botha must search for a new political identity. The 16 Nationalists are expected to form a new party, but their plans have not yet been finalized.
Six others who had opposed the prime minister later reversed their stand, and Mr. Botha said they had been accepted back without rancor.
Meanwhile, the dissidents are likely to pose in the short term less of an organized opposition to Botha than they did as members of the National Party, say many analysts.
Colin Eglin, chairman of the Progressive Federal Party (the official opposition party) concedes somewhat skeptically: ''If Mr. Botha has a reform agenda, he is more likely to proceed now.''
The two most visible issues confronting South Africa at the moment are a settlement in Namibia and the development of a new constitution granting political rights to Coloreds (persons of mixed descent) and Indians.
It was the latter issue which precipitated the split when Mr. Botha allowed last week that Colored and Indian representation could be considered ''healthy power sharing.''
The National Party has been mulling over constitutional proposals for some form of Indian and Colored political representation since 1977. But in recent months, the debate has slowly incorporated the notion of ''power sharing,'' perhaps implying a more integrated role for these nonwhite groups in the government than was anticipated in 1977.
Mr. Eglin reckons the confrontation between Mr. Botha and his right wing was deliberately brought on to pave the way for new constitutional recommendations by the President's Council.