Ngidi strained his hamstring while playing for the Titans against the Dolphins in the opening round of the domestic first-class season last week.
The 20-year-old Nqobani Mokoena has been added to the Proteas squad that will meet up for a camp on Saturday, with the ODI series against Australia set to begin on 24 September in Durban.
Ngidi is the third pace bowler to be withdrawn with Kagiso Rabada and Ottneil Baartman also in rehabilitation with hamstring injuries.
Rabada and Ngidi now racing to be fit for the Test series against Australia that starts in early October.
The Proteas pace attack in the 50-over format will now be lead by Marco Jansen with his brother Duan also in the squad, along with Corbin Bosch, Gerald Coetzee and Kwena Maphaka.
Ryan Rickelton and Temba Bavuma shone with the bat in the opening round of the domestic first-class competition, but there was an injury concern for Proteas fast bowler Lungi Ngidi who hobbled off injured.
The Proteas will be without pace bowler Ottneil Baartman for their ODI series against Australia after he injured his hamstring playing first-class cricket for the Dolphins.
The Proteas wrapped up their ODI series against Namibia with a commanding nine-wicket victory in Windhoek on Sunday, completing a 3-0 clean sweep.
Connor Esterhuizen struck his maiden ODI century as the Proteas beat Namibia by 157 runs in the second match in Windhoek, with the visitors wrapping up a series victory with a game to spare.
