Steve Smith will leave Australia's tour of Sri Lanka after Wednesday's 82-run defeat in Colombo to focus on preparing for the series with South Africa.
The Australian captain will step aside for the remaining three one-day internationals and two Twenty20 internationals, leaving David Warner to lead the side.
Wednesday's defeat left the ODI series evenly poised at 1-1, Australia bowled out for 206 as they chased 288.
Warner takes over as the tour moves to Dambulla and then Pallekele, with national selector Rod Marsh insisting Smith was always going to take a break ahead of the Proteas' visit.
"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," said Marsh.
"Regardless of the results of the first two matches 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."
Australia's first ODI with South Africa begins on September 30 in Centurion.