Yellow fever is an infectious disease caused by a virus carried by the Aëdes aegypti mosquito. South Africa does not have yellow fever but to avoid its introduction international health regulations require all travellers arriving from a yellow fever risk country to show proof that they have been vaccinated. This includes anyone whose flight included a stopover in a yellow fever risk country, even if they did not get off the plane. If you are travelling from or have passed through a yellow fever risk country in the six days before your arrival in South Africa, you must have a valid Yellow Fever Certificate.
Wikitravel includes the folowing information about yellow fever vaccinations at http://wikitravel.org/en/Yellow_fever
A vaccine is available which provides immunity for at least ten years. Many countries will require that you be vaccinated against yellow fever if you are coming from a country where it is present or have been in such a country within the last 6 days (the incubation period). If this is the case you will need to present a "World Health Organisation International Certificate of Vaccination" with an appropriately dated certification on the "International Certificate of Vaccination or Revaccination Against Yellow Fever" page to immigration officials. This little yellow booklet will be given to you when you are vaccinated against yellow fever for the first time. Carry it with your passport: you'll typically present them to immigration officials at the same time.
It is generally easiest to get a yellow fever vaccination in your home country before you leave on your trip. The vaccination is not in the normal vaccination schedules of many countries outside the infected areas since it is unnecessary unless you are travelling and has a somewhat higher risk of complications than many other vaccines. You will need to especially request a yellow fever vaccination from a designated yellow fever vaccination center. Immunity is considered to start 10 days from the time of the vaccination, so be sure to get vaccinated 10 days before you enter an infected country. The vaccine is live and not entirely inactive: many people have mild flu-like symptoms for a couple of days after receiving this vaccine, so it would be good not to be planning anything strenuous in those days.
Below is the list of countries with yellow fever risk included in the South Africa Department of Health Yellow Fever Policy Brief.
