Coach Heyneke Meyer has responded to calls to include the 20-year-old fly-half at the expense of his regular 10, the out-of-form Morne Steyn.
Goosen's selection is one of three changes, with locks Andries Bekker and Eben Etzebeth also recalled.
There could be a fourth alteration too, with Francois Steyn battling an ankle injury and Jaco Taute standing by.
South Africa team to face Australia: Zane Kirchner; Bryan Habana, Jean de Villiers, Francois Steyn, Francois Hougaard; Johan Goosen, Ruan Pienaar; Tendai Mtawarira, Adriaan Strauss, Jannie du Plessis, Eben Etzebeth, Andries Bekker, Francois Louw, Willem Alberts, Duane Vermeulen.
Replacements: Tiaan Liebenberg, Coenie Oosthuizen, Flip van der Merwe, Marcell Coetzee, Elton Jantjies, Jaco Taute, Pat Lambie.