Pact began operating in South Africa in 1991 with the aim to strengthen the South African NGO sector, specifically to build new NGO leadership and train a new cadre of South Africans to serve the needs of NGOs, and continued programming in that area until 2001.

As NGOs gradually made the transition from fighting apartheid to building a new country, Pact assisted them to identify new visions and missions for their organizations. Through a dynamic organizational development and strategic management training course, NGO leaders learned to increase their leadership effectiveness and organizational management skill in order to shoulder greater responsibility at the local and national level and thus rebuild the NGO sector.

In addition to the training course, Pact seconded an NGO advisor to the office of South Africa Deputy President Thabo Mbeki to bridge the gap between NGOs and government in provision of development services, leading to the establishment of the National Development Agency, which was established to provide grants to NGOs and serve as a mechanism for dialogue between NGOs and government.

Finally Pact launched the Sedibeng Centre for Organizational Effectiveness in 1997, a South African NGO that aimed to carry forward Pact's NGO strengthening activities and contribute towards building democracy and civil society.

Under the South Africa Transition Support Fund (1995-2001), Pact developed a program to strengthen the grant-making capacity of South African NGOs to manage umbrella grants. Training covered the complete cycle of grant-making from solicitation to reporting and close-out; USAID regulations, policies and procedures for grants and financial management; the role of boards in carrying out responsibility for vision, policy oversight and accountability; and financial sustainability, including endowments, investments and competitive bidding. Pact then closed its doors in 2001.

After a two-year hiatus in operations, Pact reopened its programming in South Africa in 2003 with a USAID-funded project to strengthen CBO partnerships with local governments to improve policy development and service delivery.

Working in partnership with Action Aid Pact employed a highly focused set of training and support interventions for CBOs to increase public participation in local government and creating partnerships for development with local councils. The project also focused on strengthening the capacity of criminal justice and victim empowerment CSOs and civil society responses to fight corruption.

In early 2004 under the auspices of the USAID's Community REACH Rapid Response Mechanism Pact was asked to provide grants and administrative services to support HIV/AIDS projects at the community level in South Africa. Subsequently Pact was also asked to manage The South Africa Regional HIV/AIDS program, which covers Swaziland, Lesotho and Botswana under a cooperative agreement with USAID South Africa's Regional HIV/AIDS Program for Southern Africa (RHAP).