Why didn’t the Portuguese colonise South Africa?

To understand the Portuguese presence in Africa in the 16th Century, it's important to understand that at no time did they think of colonizing in the sense of founding a settlement that they intended to bring large numbers of Portuguese citizens to or that the Portuguese crown would claim direct territorial sovereignty over. The same could be said of the Dutch East India Company in Cape Town, in fact--the goal of the company's initial post was not to create a colonial settlement that would expand or create a larger dominion over time. That was on some level an accident of the VOC allowing company employees to claim land for farming in the vicinity of the trading post after their term of service was complete.

But the Portuguese did have a considerable presence in what is now Congo, Angola and Mozambique and in those cases did engage in activities closer to what we conceptualize as colonialism--they deployed troops and claimed territory as well as some form of authority over indigenous rulers, and in the case of Congo and Angola, also drew local societies heavily into the Atlantic slave trade. So the question really is, "Why not the Western Cape as well?"

In part it comes down to how the 16th Century Portuguese captains and crews who got as far south as the Cape and beyond into the Indian Ocean looked at their objectives. Congo and Angola (and points further north in West Africa where the Portuguese had a presence) were valuable in the context of Atlantic exchange for slaves but also for gold, leather and other commodities that the Portuguese valued. As the 16th Century wore on, that value began to shift towards slavery but the Atlantic system was still some ways from being centrally defined by enslavement. The Portuguese presence in Mozambique and up the coast from there was about two things: trying to get access to gold being produced by the Munhumutapa state in what is now Zimbabwe via extending Portuguese presence up the Zambezi valley and about establishing a commercial presence in East African trading towns that were an important part of Indian Ocean trade.

The Western Cape by comparison offered little of immediate or obvious value to the Portuguese. Local Khoikhoi pastoralists were sometimes willing to trade with Portuguese crews (and later, Dutch crews) but were also sometimes hostile to their presence (for good reason, as both groups of sailors were sometimes prone to just take what they wanted, cattle in particular). Portuguese crews could see the value of the Western Cape from the standpoint of rewatering and refreshing their food supplies, but they didn't otherwise see the region as offering much that would justify the risks and expense of an outpost at a time when Portuguese manpower was in short supply and in demand in many other locations in the Americas, Africa and the Indian Ocean world. St. Helena was deemed just as useful for refreshment, in part because of the way that ships heading southward down the western coast of Africa had to sail well off-shore and back again in order to continuously catch winds.

It was by no means certain that the Dutch East India Company (VOC) would establish its refreshment post in Cape Town--the initial proposal to do so had to overcome a number of objections (the possible hostility of indigenous people, the question of whether or how the station would be better than St. Helena, which by 1652 was in VOC hands, and the question of how to staff the post, considering that the company's truly valuable operations were elsewhere). All the things that came to be seen as valuable about the Western Cape as a site of colonial conquest and settlement were not evident to 16th and early 17th Century mercantile companies--and indeed, the VOC often continued to see the Cape as a source of annoyance and distraction even after 1652.