The South African-born batsman has been a stalwart of the Australia ODI team since 2022 and helped them win a sixth World Cup in India three years ago.
The 32-year-old right-hander averages 21.87 with a high score of 77 not out in the 50-over format since the start of 2024, however, and there was no place for him in the 17-man squad for six ODIs announced on Tuesday.
Chief selector George Bailey declined to speculate on Labuschagne's future in the test team, which is also under threat after a poor run of form, but stressed the importance of the upcoming ODI tour for World Cup preparations.
"We're separating those formats out so this was a one-day cricket conversation," he told reporters via a video call.
"I think this is a pretty important tour for us. It's hard to get the link, but Zimbabwe and South Africa, that's where the World Cup will be played late next year.
"There's not a whole lot of (ODI) games (before that) and the opportunity that's ... awarded to some of those other players to continue building out their roles ... will be really important.
"(Marnus), again, he's played some really important one-day cricket for us, at his best. That looks a certain way, but the way that squad and team is structuring up, there just wasn't space for him."
All-rounder Mitchell Marsh, opener Travis Head and paceman Josh Hazlewood all return to the squad after missing Australia's most recent ODI outings against Bangladesh.
Fast bowlers Pat Cummins and Mitchell Starc will join the squad for the three ODIs against South Africa, which follow a similar number of matches in Zimbabwe.
Uncapped Joel Davies and fellow youngsters Oliver Peake and Cooper Connolly were all included in the party for the tour, which begins against Zimbabwe in Harare on September 15.
The squad for the three tests in South Africa in October will be named later this month.
"We just we're still working through what that test squad is going to look like and exactly what we feel we'll need in South Africa," said Bailey.
Australia ODI squad:
Xavier Bartlett, Alex Carey, Cooper Connolly, Pat Cummins, Joel Davies, Nathan Ellis, Cameron Green, Josh Hazlewood, Travis Head, Josh Inglis, Spencer Johnson, Mitchell Marsh, Oliver Peake, Matt Renshaw, Billy Stanlake, Mitchell Starc, Adam Zampa