Beginning in 1948 following the general election, the party as the governing party of South Africa began implementing its policy of racial segregation, known as apartheid (the Afrikaans term for "separateness"). Although White-minority rule and racial segregation were already in existence in South Africa with non-Whites not having voting rights and efforts made to encourage segregation, apartheid intensified the segregation with stern penalties for non-Whites entering into areas designated for Whites-only without having a pass to permit them to do so (known as the pass laws), interracial marriage and sexual relationships were illegal and punishable offences. Black people faced significant restrictions on property rights. After South Africa was condemned by the British Commonwealth for its policies of apartheid, the NP-led government had South Africa leave the Commonwealth, abandon its monarchy led by the British monarch and become an independent republic. The party's system of apartheid was officially labelled a crime against humanity by the United Nations General Assembly on 16 December 1966.


During the 1970s and 1980s, the NP-led white apartheid government faced internal unrest in South Africa and international pressure for the accommodation of non-Whites in South Africa. It resulted in policies of granting concessions to the non-White population while still retaining the apartheid system, such as the creation of Bantustans that were autonomous self-governing Black homelands (criticised for several of them being broken up into unconnected pieces and that they were still dominated by the White minority South African government), removing legal prohibitions on interracial marriage, and legalising certain non-White and multiracial political parties (excluding the very popular African National Congress (ANC), which the government still viewed as a terrorist organisation). Those identified as Coloureds and Indian South Africans were granted separate legislatures in 1983 alongside the central legislature that represented Whites to provide them self-government while maintaining apartheid, but no such congress was supplied to the Black population as their self-government was to be provided through the Bantustans. The NP-led government began changing laws affected by the apartheid system that had come under heavy domestic and international condemnation, such as removing the pass laws, granting Blacks full property rights that ended previous significant restrictions on Black land ownership, and the right to form trade unions. Following escalating economic sanctions over apartheid, negotiations between the NP-led government led by P. W. Botha and the outlawed ANC led by then-imprisoned Nelson Mandela began in 1987 with Botha seeking to accommodate the ANC's demands and consider releasing Mandela and legalising the ANC on the condition that it would renounce the use of political violence to attain its aims.


In the 1989 South African general election, the party under F. W. de Klerk's leadership declared that it intended to negotiate with the Black South African community for a political solution to accommodate Black South Africans. This resulted in De Klerk declaring in February 1990 the decision to transition South Africa out of apartheid, and permitted the release of Mandela from prison and ending South Africa's ban on the ANC and other anti-apartheid movements, and began negotiations with the ANC for a post-apartheid political system. In September 1990 the party opened up its membership to all racial groups and rebranded itself as no longer being an ethnic nationalist party only representing Afrikaners, but would henceforth be a civic nationalist and conservative party representing all South Africans.^[6] However, there was significant opposition among hardliner supporters of apartheid that resulted in De Klerk's government responding to them by holding a national referendum on Apartheid in 1992 for the White population alone that asked them if they supported the government's policy to end apartheid and establish elections open to all South Africans: a large majority voted in favour of the government's policy. In the 1994 elections, it expanded its base to include many non-Whites, including significant support from Coloured and Indian South Africans. It participated in the Government of National Unity between 1994 and 1996. In an attempt to distance itself from its past, the party was renamed the New National Party in 1997. The attempt was largely unsuccessful and the new party decided to merge with the ANC.