Captain Steve Smith will fly home from Sri Lanka following Australia's defeat in the second ODI in Colombo, with national selector Rod Marsh deciding to rest the 27-year-old.
Smith will miss the remaining three one-day fixtures and two T20s, with vice-captain David Warner to take the reins for the first time.
Smith plays all three formats of the game and Marsh wants to allow him time to prepare for the upcoming five-match one-day series in South Africa starting with a one-off game against Ireland on September 27 in Benoni.
"I hate missing cricket but in the long run it will do me a world of good," Smith said following his side's 82-run loss on Wednesday that saw the hosts level the series 1-1.
"The schedule is very busy. I still want to take on the role in all three formats and do it to the best of my ability."
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Smith has skippered the side for the past 24 ODIs having replaced Michael Clarke following the Cricket World Cup triumph last year and Warner will become only the 23rd man to lead the Australian team in the third match in Dambulla on Sunday.
Marsh said it was always part of his plan to give Smith a rest, regardless of the state of the current series which followed a dismal 3-0 Test whitewash by Sri Lanka.
"Steve has a large amount of cricket coming up in the next 12 months and we wanted to find a time for him to freshen up and these last five matches provide a good opportunity to do so," Marsh said.
"Our plan was always for Steve to take a break and refresh ahead of the ODI series against South Africa next month.
"This is a great leadership opportunity for David, he has really embraced his role as vice-captain and we are confident he will do a great job in Steve's place."
Smith will be joined in returning to Australia by Nathan Coulter-Nile, who succumbed to a lower-back injury on Thursday.
The paceman will return to Perth for further analysis after increasing pain prevented him bowling at match intensity.
Coulter-Nile, who has been plagued by injuries at crucial times throughout his career, has not played a game on the tour and will not be replaced.
