There are a number of Australian Embassies in Africa. There are also a number of Honorary Consulates such as the Australian Consulate in Windhoek as well as an Australian Consulate in Tanzania. You will need to email or call them first to ensure that you have all the needed documents if you wish to apply for an Australian visa while in the country.
Note also that you will needed to ensure that they are open as the Australian offices close of both local public holidays as well as on Australian public holidays. The Australian High Commission in South Africa would be one of the biggest representative offices on the continent. See the listings of the most widely used representative offices on the continent. See also the other listing for Australian Embassies in Asia as well as in South America.