Hendricks, who has five Twenty20 caps to his name, was originally named in the 15-man squad for the three-match rubber, but has been withdrawn due to a lumbar strain suffered during South Africa A's tour of Australia.
No replacement will be drafted in for Hendricks as South Africa already have four other seam bowlers in their selection.
Marchant de Lange, Kyle Abbott, Wayne Parnell and the uncapped Mthokozisi Shezi are in contention to lead the attack in the absence of Dale Steyn, Morne Morkel and Vernon Philander, who have all been rested following the successful Test campaigns against Sri Lanka and Zimbabwe.
However, that trio will return for the triangular series with Zimbabwe and Australia, which starts on August 25.
All of the matches in the ODI series are to take to place in Bulawayo, with the opening game to be held on Sunday.