South Africa beat Zimbabwe by 61 runs in the second ODI to clinch the three-match series on Tuesday in Bulawayo.
The Proteas Test captain has been given a few days off, before returning to action next week in the triangular series also involving Australia in Harare.
Amla’s absence is set to give an opportunity to the likes of Rilee Rossouw, Mthokozisi Shezi and Marchant de Lange, who are yet to receive game time in the series.
Captain AB de Villiers said he was impressed with the batting depth shown by the lower order in the series-winning performance.
“It wasn’t a bad batting performance considering that our top order didn’t score a lot of runs,” De Villiers said.
“The fact that Wayne Parnell and some of the middle order and tail chipped in a lot was pleasing. It shows that there is a lot of depth in the batting order.”
De Villiers backed the decision to rest Amla for the third ODI in Bulawayo.
“He has played a lot of cricket and scored a lot of runs, so it will be a good opportunity for him to take some time off for one game and get him back here for the tri-series nice and fresh.”