Neither man featured in South Africa's 3-0 one-day international series win over Zimbabwe, sealed with a seven-wicket success in Bulawayo on Thursday.
And Cricket South Africa (CSA) confirmed that the duo will play no part in the triangular tournament, with South Africa's first match coming against Australia in Harare on Wednesday.
Mthokozisi Shezi made his debut in Thursday's win and he and Kyle Abbott will take the places of the sidelined duo. Philander continues to struggle with a hamstring problem, while Hendricks is out with a back injury.
"Kyle impressed in the three matches he played against Zimbabwe while Mthokozisi, who also did well on his debut, is a like-for-like replacement for Beuran," said CSA selection chief Andrew Hudson.
"It was also pleasing to see Marchant de Lange resume his international career so well after a lengthy injury break and he underlines the tremendous depth we have to our fast bowling resources at the moment."
To underline Hudson's point, first-choice seamers Dale Steyn and Morne Morkel re-join the squad after being rested for the three matches against Zimbabwe.