Jones who sustained a tear to his calf muscle playing for the Ospreys in their defeat to Glasgow at the weekend.
Jones will be re-assessed after the Australia match but Rees will become the 128th player to lead his country when the November tests begin a week on Saturday.
"It's obviously a huge honour to captain your country and it's something that probably won't really sink in until we get to match-day," said Rees.
"To lead the side out at the Millennium Stadium against a side of the strength and stature of Australia is just an amazing thought,"
"I hope to be able to take it all in my stride and as a squad we are certainly looking to perform against the Wallabies and come away with the right result to kick-off our Autumn campaign, and this Rugby World Cup season, in the right way."
Rees was handed the captaincy at Parc Y Scarlets at the start of the season and his side's victory in the Welsh derby against the Blues at the weekend lifted the region into second in the Magners League table.
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