Due to a calf injury, Buttler, 33, has not participated in competition since the T20 World Cup in June.
Harry Brook is ready to step up if necessary in the ODIs, but Phil Salt will skipper England for the first time in the T20s in his absence.
The ODIs begin on September 19, and the T20 series kicks out in Southampton on Wednesday.
Australia’s visit marks England’s first white-ball assignment following their elimination from the T20 World Cup semifinals.
Since then, head coach Matthew Mott has departed, although captain Buttler has stayed in place following a managing director review.
England’s temporary white-ball coach for the Australia series and the November West Indies tour is Marcus Trescothick.
Brendon McCullum, the Test coach, was named this week to lead the limited-overs teams; however, his combined duty won’t start until January.
Before The Hundred, Buttler sustained an injury during practice. He missed the entire tournament, as well as Lancashire’s loss to Sussex in the T20 Blast quarterfinals on Wednesday.
