The 31-year-old injured his finger while keeping wicket in South Africa’s 67-run win in the first ODI played in Durban on Thursday.
No replacement in the ODI squad has been named, with Alex Carey expected to don the gloves in the second fixture in the series in Johannesburg on Sunday.
Inglis is now in a race to be fit for the three-match Test series in South Africa that starts on October 9.
Cricket Australia confirmed Inglis would return to Perth for treatment, "with his availability for the three-match Test series subject to further assessment and progress".