A single species of Penguin, Spheniscus demersus, or the Blackfooted Penguin, lives in Southern Africa today, though two species, Nucleornis insolitus and Inguza predemersus are known to have lived there in the Early Pliocene. It has generally been assumed that the modern Penguins are descendants of the fossil penguins, though since they are also clearly closely related to other Penguins of the genus Spheniscus, which live in South America and the Galapagos, it is difficult to say what the exact relationship is.
Issue 279 of the Proceedings Of The Royal Society B contains a paper by Daniel Ksepka of the Department of Marine, Earth and Atmospheric Sciences at North Carolina State University and the Department of Zoology at the University of Cape Town and Daniel Thomas of the Department of Paleontology at North Carolina Museum of Natural Sciences in which they describe the results of a thorough investigation into South Africa's Penguins and the conclusions derived from this.
Reconstruction of the Pliocene Penguin Inguza predemersus (right) with a modern Blackfooted Penguin (left) for scale. From Ksepska and Thomas (2012).
Ksepska and Thomas examined over 200 fossil Penguins from the Iziko South African Museum collections, and compared them to recent and fossil penguins from South Africa and elsewhere. The came to the conclusion that modern Blackfooted Penguins are closely related to the Chinstrap Penguins of South America and the Galapagos, but not closely related to either of the fossil Penguins, and certainly not descended from either. Nor are the two extinct forms closely related.
This means that Penguins have invaded Africa on at least three separate occasions, something that Ksepska and Thomas examined next. Penguins appear first in the fossil record of New Zealand, but by the end of the Eocene are widespread in Antarctia, Australia and South America. They do not appear in Africa until the Early Pliocene, 30 million years later, and have never reached Madagascar of the Northern Hemisphere.
The inability of Penguins to colonize the Northern Hemisphere is the easiest to explain. Currents around the equator tend to flow away from it; in the Northern Hemisphere to the north and in the Southern Hemisphere to the south. There are also strong thermoclines to cross; water forms 'streams' within the ocean (such as the Gulf Stream) dependent on temperature, things flow easily within these streams, but it is hard to cross from one to the other. Similarly Madagascar is separated from Africa by the strong Agulhas Current, which sweeps away from Madagascar.
Africa can be reached from South America by the South Atlantic Current and the Antarctic Circumpolar Current, but these currents have not always flowed on their current paths. Prior to the Pliocene Antarctica and South America were still connected together; the Antarctic Peninsula was attached to the tip of Patagonia. This stopped the flow of the Antarctic Current, and trapped Penguins in the South Pacific. After the continents broke apart the Penguins were free to colonize the South Atlantic and soon reached Africa.
Map of the South Atlantic showing the prevalent currents and fronts. Dots show the location of modern Blackfooted Penguin colonies, and open stars locations where fossil Penguins have been found. From Ksepska and Thomas (2012).
Next Ksepska and Thomas looked at the extinction of the Pliocene Penguins. It is of course impossible to state the exact causes of such extinctions with absolute confidence, but this does not stop scientists from attempting to come up with plausible scenarios. During the Early Pliocene the sea-level was about 90 m higher than it is now. At the end of the Early Pliocene it dropped sharply, due to the increasing glaciation of Antarctica; another consequence of the separation of South America and Antarctica, which enabled the developing Circumpolar Current to isolate the southern continent in its own climatic zone, and caused the temperature to plummet. Ksepska and Thomas theorize that the Pliocene African Penguins may have been dependent on offshore islands as breeding grounds, and that either the falling waters left them vulnerable to African predators that they were unable to cope with, or that fluctuating sea levels associated with the changing climate left them unable to find safe nesting sites.
See also Was Archaeopteryx black? A new fossil bird from the Palaeocene of Brazil, Giant Bird from the Cretaceous of Kazakhstan, New 'oldest bird' found in China and Birds on Sciency Thoughts YouTube.