First of all discrimination against the indigenous people of Southern Africa didn't start with apartheid so basically it can't be blamed solely on the apartheid system, although the apartheid system intensified racial tension and discrimination of the Black population.

The kapkolonie or cape colony as it was called prior to British occupation wasn't a traditional African colony because the primary purpose was not the slave trade nor the not yet discovered mineral resources but the sole location on the world map. Every European empire was racing to India during the 17th century, hence passing the southern part of Africa atleast twice on their way. Therefore mostly exiled(Dutch and French protestants) Europeans and people who abandoned their ship for hope of a better life lived and were part of the colony from 1652 until British occupation in 1795.

During this time obviously slavery and slave trade was a common thing, especially agricultural slaves were very common as the cape colony consisted of mostly farmers and what is now Capetown but slaves were also present in and around households of their owners and performed various traditional labour's. In addition grew the acquisition of slaves through the indigenous population by demand and needed supply. Little to no sources can confirm an existing (out of proportion) discrimination during this time of the colony but seeing how slavery worked around the globe and especially in Africa one can assume that basic human or even slave rights were not regularly looked after. During the British rule of Southern Africa blacks received the same treatment as before only the ruling party changed. The newly discovered rich land resources and agricultural aspect of South Africa (huge fertile landspaces) gained focus with slavery being the driving force behind agricultural and military advances of British South Africa. Slavery was officially abolished in 1833 but as other British colonies the cape colony didn't enforce anti-slavery rules to the end of it.

To answer your question, slavery existed prior to the apartheid system, hence discrimination towards specific populations surely existed aswell but there is no indication of a level of discrimination like the apartheid system enabled. But it's history definitely is one of the reasons the apartheid system enforced such unparalleled segregation and discrimination towards its black population.

Sources: Beck, Roger(2000): The History of South Africa Elbourne, Elizabeth(2002): Blood Ground: Colonialism, Missions, and the contets for Christianity in the cape colony and Britain, 1799-1853