Botha passed away peacefully in his sleep just after 8:00 pm (0500AEDT) at his home in the town of Wilderness in the Western Cape, according to members of his staff and family friends.
"Botha died at home, peacefully," one of his security officers, Frikkie Lucas, told the SAPA news agency.
Botha, nicknamed the "Groot Krokodil" (Afrikaans for the "Great Crocodile") for his tough and uncompromising stance on politics, led white minority rule of South Africa between 1978 and 1989.
He first entered parliament as MP for the coastal town of George in 1948, when the National Party (NP) took power in South Africa, marking the official start of apartheid.
After a scandal forced the resignation of then prime minister John Vorster in 1978, Botha slipped into his shoes, winning on a split vote within the party.
He quickly moved to impose a steel grip on political power called
"kragdadigheid" (Afrikaans for "using brute force to achieve political goals").
He defied the world during the turbulent and violence-wracked period and turned a deaf ear to mounting international condemnation of the horrors of the apartheid system.
The National Party leader stood down in favour of F.W. de Klerk who later steered South Africa towards the country's first multi-racial elections in 1994 which were won by Nelson Mandela's African National Congress (ANC).
The National Party has since folded and its last leader, Marthinus van Schalkwyk, is now a member of the ANC government.
ANC expresses 'sorrow'
The ANC, which has ruled South Africa since 1994, expressed its condolences over the death of its one-time arch-enemy.
"The ANC wishes his family strength and comfort at this difficult time," it said in a statement.
Adriaan Vlok, who served as law and order minister under Botha, spoke of his sorrow at the news of his former leader's death.
"I was very sorry to hear about Mr Botha's death. I extend my deepest sympathies to his family," he said.
"I will remember many things about him, foremost that he was a very disciplined person. And he loved people. He loved his people and he loved children."
Botha's death comes barely a fortnight after he was treated in hospital for what doctors said at the time was a routine check-up, denying reports that he had suffered another stroke after the first one in 1989 that forced him out of politics.