The experienced batsman, a key pillar of their World Cup-winning side in 2023, paid the price for poor recent form with his future as a Test player also on the line.
Australia play three ODIs in Zimbabwe and another three in South Africa this month, before a three-Test series against the Proteas in Durban, Gqeberha and Cape Town in October.
The Test squad will be named at a later date.
With Australia's World Cup defence just a year away, selectors included batting prodigy Peake, 19, and talented all-rounders Davies, 22, and Connolly, 23, as they usher in a new generation.
Mitch Marsh, fellow opener Travis Head and quick Josh Hazlewood return after missing ODI series in Pakistan and Bangladesh earlier this year.
Fast bowlers Pat Cummins and Mitchell Starc will only play the three matches in South Africa as their workloads are managed.
But there are plenty of other pace options with Spencer Johnson, Nathan Ellis, Xavier Bartlett and Billy Stanlake all in the 17-player touring party.
Adam Zampa is the only specialist spinner, with Matthew Kuhnemann dropped.
"This six-game series is an important lead-in to next year's World Cup, being played in the same countries, for the group," said chief selector George Bailey.
"As such it's great to have Mitch (Marsh), Travis and Josh returning, then Pat and Mitch (Starc) for the SA leg. This gives us our core of players mixed with some we think will continue to make an impression.
"For Ollie and Joel, who we rate very highly, it's another fantastic opportunity and a further chance for them to continue their exposure and growth in the Australian team."
Selectors also named an Australia A squad for a tour of India later this month, which will feature two four-day matches and three one-dayers against India A.
With Labuschagne's Test place at risk, Peter Handscomb and Nathan McSweeney will be looking to impress ahead of the senior team's five-Test tour of India in January-February.
Speedsters Brendan Doggett and Jhye Richardson add plenty of firepower.
Australia ODI squad for Zimbabwe and South Africa:
Mitchell Marsh, Pat Cummins (South Africa only), Xavier Bartlett, Alex Carey, Cooper Connolly, Joel Davies, Nathan Ellis, Cameron Green, Josh Hazlewood, Travis Head, Josh Inglis, Spencer Johnson, Ollie Peake, Matt Renshaw, Billy Stanlake, Mitchell Starc (South Africa only), Adam Zampa
Australia A four-day squad for India:
Brendan Doggett, Jack Edwards, Peter Handscomb, Sam Harper, Liam Hatcher, Campbell Kellaway, Sam Konstas, Nathan McSweeney, Todd Murphy, Fergus O'Neill, Josh Philippe, Jhye Richardson, Corey Rocchiccioli, Jason Sangha, Liam Scott
Australia A one-day squad for India:
Mahli Beardman, Nikhil Chaudhary, Ben Dwarshuis, Jack Edwards, Aaron Hardie, Spencer Johnson, Sam Konstas, Nathan McSweeney, Todd Murphy, Mitch Owen, Josh Philippe, Tanveer Sangha, Liam Scott, Lachlan Shaw