The 37-year-old Dhoni has been the team's mainstay after making his mark as a wicketkeeper-batsman and later as leader in all the three formats.
But Dhoni, who led India to its inaugural World T20 triumph in 2007 and the 50-over World Cup title in 2011, finds his name missing in the 16-member T20 squads.
Meanwhile skipper Virat Kohli has been rested for the three T20 matches against West Indies starting November 4 in Kolkata and will return for the Australia series.
Emerging wicketkeeper-batsman Rishabh Pant and Dinesh Karthik have been named in both the T20 squads with a possible eye on grooming Dhoni's successor.
Dhoni has represented India in 90 Tests, 329 ODIs and 93 T20 matches since making his debut in 2004 in a one-day game against Bangladesh in Chittagong.
The player once dubbed "Captain Cool" retired from Tests in 2014 and then relinquished the limited-overs captaincy in 2017.
The first of three T20 matches in Australia will be played in Brisbane on November 21 before the teams move to four Tests and four one-day internationals.
The Indian selectors have included batsman Rohit Sharma and opener Murali Vijay for the Test matches starting December 6 in Adelaide.
Wicketkeeper-batsman Parthiv Patel is also part of the 18-member Test squad while injured all rounder Hardik Pandya has still not recovered to feature in the team.
Rohit Sharma (captain), Shikhar Dhawan, Lokesh Rahul, Dinesh Karthik, Manish Pandey, Shreyas Iyer, Rishabh Pant (wicket-keeper), Krunal Pandya, Washington Sundar, Yuzvendra Chahal, Kuldeep Yadav, Bhuvneshwar Kumar, Jasprit Bumrah, Khaleel Ahmed, Umesh Yadav, Shahbaz Nadeem
Virat Kohli (captain), Rohit Sharma (vice-captain), Shikhar Dhawan, Lokesh Rahul, Shreyas Iyer, Manish Pandey, Dinesh Karthik, Rishabh Pant (wicket-keeper), Kuldeep Yadav, Yuzvendra Chahal, Washington Sundar, Krunal Pandya, Bhuvneshwar Kumar, Jasprit Bumrah, Umesh Yadav, Khaleel Ahmed
Virat Kohli (captain), Murali Vijay, Lokesh Rahul, Prithvi Shaw, Cheteshwar Pujara, Ajinkya Rahane (vice-captain), Hanuma Vihari, Rohit Sharma, Rishabh Pant (wicket-keeper), Parthiv Patel (wicket-keeper), R Ashwin, Ravindra Jadeja, Kuldeep Yadav, Mohammed Shami, Ishant Sharma, Umesh Yadav, Jasprit Bumrah, Bhuvneshwar Kumar