Maphaka joins fellow seamers Kagiso Rabada, Lungi Ngidi and Ottneil Baartman that have sustained hamstring injuries in recent times.
Lizaad Williams has been drafted into the Proteas' 16-man squad as a replacement for Maphaka, while Duan Jansen and Nqobani Mokoena came in for Ngidi and Baartman.
The Proteas pace attack for the 50-over encounters will have an inexperienced feel to it with Marco Jansen leading the way with 32 ODI caps, while Corbin Bosch and Gerald Coetzee having played 14 ODIs apiece.
The 32-year-old Williams last made an appearance in the 50-over for the Proteas in November last year and has eight caps to his name having made his debut in 2021.
The ODI series against Australia starts in Durban on Thursday, with further matches at the Wanderers on Sunday and Potchefstroom on 30 September.
The Proteas will be sweating on the fitness of Rabada and Ngidi for the three-match Test series against Australia that is set to begin in Durban on 9 October.
Updated Proteas squad: Temba Bavuma (captain), Corbin Bosch, Matthew Breetzke, Gerald Coetzee, Quinton de Kock (wk), Tony de Zorzi, Bjorn Fortuin, Duan Jansen, Marco Jansen, Nqobani Mokoena, Keshav Maharaj, Aiden Markram, David Miller, Ryan Rickelton (wk), Tristan Stubbs, Lizaad Williams
Aiden Markram says it was "nice having a little bit of time off" but is ready to contribute as the Proteas eye an ODI series victory against Australia at the Wanderers on Sunday.
David Miller produced a career-best innings and Temba Bavuma added a century while the spinners dominated for the Proteas as they secured a second consecutive victory over Australia, winning the second ODI by 32 runs at the Wanderers in Johannesburg.
Anrich Nortje has been selected in an expanded 18-man Proteas Test squad for the series against Australia despite having not played a red-ball game in three years, while Kagiso Rabada is also included.
South Africa recovered from a difficult start to defeat Australia by 67 runs in the first ODI in Durban, taking an early lead in the three-match series.
