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
Australian stars Cameron Green and Matt Renshaw appeared to have added their names to the growing injury list during the third and final ODI against the Proteas on Wednesday night.
Australia avoided a 3-0 ODI series defeat as rain brought South Africa’s chase to an early end in Potchefstroom on Wednesday.
Proteas spinner Keshav Maharaj has jumped up to third in the latest ICC ODI bowling rankings after impressing in the first two games of the home series against Australia.
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.
