Australia are due to play four one-dayers in Harare in August and September, two against each African nation, as well as a potential final.
Clarke said the tour was a crucial step in the team's preparations for next year's World Cup and he wants as strong a team as possible alongside him.
"It's an important series," he told reporters.
"Any one-day game now leading up to the World Cup is crucial to us as a team.
One player who will not be on tour is opener Warner, who has pulled out citing a draining playing schedule and the upcoming birth of his first child.
Australia get their tour underway against Zimbabwe on August 25 before meeting South Africa two days later, who will continue to be led in the limited-overs format by AB de Villiers.
Hashim Amla was named as the successor to Graeme Smith as South Africa's Test captain yesterday.
"I was surprised but in saying that, I think Hashim is obviously a wonderful player," he said.
"I've enjoyed the challenges I've had against him and I think he'll do a fantastic job for South Africa.
"South African cricket is in great hands under Hashim.
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