The idea of founding a Catholic university in South Africa started in 1993 when a group of Catholic academics, clergy and business people began discussing it. A Board of Trustees was set up in June 1997 and a Section 21 Company in November 1997.

During that period of exploration, the working groups gave serious consideration to the possibility of setting up a university in association with another university such as the Open University in the United Kingdom or another university in South Africa. In the end, legislation was enacted that made it possible to create private universities in South Africa and the working group preferred to become an independent South African university without having to have its degrees accredited by any other institution.

The name 'St Augustine' was chosen in order to indicate the African identity of the institution and because St Augustine of Hippo (354 - 430 AD) was one of the first and one of the greatest Christian scholars of Africa. In January 1999 a formal application to establish a private university was submitted to the national Department of Education. On 5th July 1999 St Augustine College was given conditional permission by the Department of Education to function as a private higher education institution and to offer the degree of Master of Philosophy in five different fields and the degree of Doctor of Philosophy also in five different fields, which degrees were duly accredited by that Department. The founding Grand Chancellor of the College was Archbishop Buti Tlhagale (1999-2010) (pictured right). The founding President of the College was Professor Edith Raidt (1999-2008) (pictured left), the first Chairman of the Board of Directors was Dr Conrad Strauss (1999-2009) (pictured right), and the first Registrar, Ms Felicity Eggleston. 

When the College was opened on 13 July 1999 by the Deputy Minister of Education, it started teaching its first students that same month. While the College started off in a small way with postgraduate degrees, one of its most important aims is to expand to a broader range of disciplines at undergraduate level. The College will continue to press for recognition as an independent university.

When the College opened in July 1999 it was situated on rented property on the site of the old Union Observatory in Johannesburg with historic Sir Herbert Baker buildings. At the end of 2001, the College was able to purchase the Holy Family Centre at 53 Ley Road in Victory Park, Johannesburg and moved at the end of January 2002 to its own campus in an equally lovely setting with more space. The purchase was made possible by a generous donation of the Catholic Diocese of Rottenburg-Stuttgart in Germany.