Fast bowler Kagiso Rabada will miss the series with injury but is hoping to be ready for the test matches that follow.
Ottneil Baartman, Kwena Maphaka, Lungi Ngidi, Corbin Bosch and Marco Jansen make up the fast bowling stocks.
Dewald Brevis has not been selected with Matthew Breetzke, David Miller and Tristan Stubbs preferred as middle-order batting options.
Bjorn Fortuin and Keshav Maharaj are the two specialist spin options in the squad.
Top order batter Aiden Markram will only be available for the second and third matches in the series.
"With the World Cup just over a year away, this series marks an important step in shaping the squad as we build towards the tournament, while also giving those players who are in the frame opportunities when we face Bangladesh and England later in the season," coach Shukri Conrad said.
The series against Australia gets under way in Durban on September 24, before the second match in Johannesburg on September 27 and then Potchefstroom on September 30.
South Africa and Australia have met in 113 ODIs in the past, with the Proteas leading the head-to-head 57-52, with three ties and one match abandoned. In South Africa, the home side lead 28-22.
Squad: Temba Bavuma (captain), Ottneil Baartman, Corbin Bosch, Matthew Breetzke, Gerald Coetzee, Quinton de Kock, Tony de Zorzi, Bjorn Fortuin, Marco Jansen, Keshav Maharaj, Kwena Maphaka, Aiden Markram, David Miller, Lungi Ngidi, Ryan Rickelton and Tristan Stubbs