Gill replaces Rohit Sharma who remains in the squad along with batting stalwart Virat Kohli.
Both Rohit and Kohli have quit test cricket and T20 Internationals and are only available for India in the 50-over format.
Gill took over as test captain after Rohit quit the long format in May, and he is vice captain of India's T20 squad led by Suryakumar Yadav.
Rohit and Kohli last played for India in the Champions Trophy final in March beating New Zealand.
Wicketkeeper-batsman Rishabh Pant, who is recovering from a fractured foot and was ruled out of the ongoing Test series against West Indies, was not selected for the Australian tour.
India will play the three ODIs in Australia followed by five T20 Internationals.
The tour begins on October 19 with the first 50-over match in Perth followed by games in Adelaide and Sydney.
The T20 series kicks off on October 29 at Canberra's Manuka Oval.
India ODI squad: Shubman Gill (capt), Rohit Sharma, Virat Kohli, Shreyas Iyer, Axar Patel, KL Rahul, Nitish Kumar Reddy, Washington Sundar, Kuldeep Yadav, Harshit Rana, Mohammed Siraj, Arshdeep Singh, Prasidh Krishna, Dhruv Jurel and Yashasvi Jaiswal
India T20 squad: Suryakumar Yadav (capt), Abhishek Sharma, Shubman Gill, Tilak Varma, Nitish Kumar Reddy, Shivam Dube, Axar Patel, Jitesh Sharma, Varun Chakaravarthy, Jasprit Bumrah, Arshdeep Singh, Kuldeep Yadav, Harshit Rana, Sanju Samson, Rinku Singh and Washington Sundar.
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