India have made three changes to the side that lost the first Test in Adelaide.
Wriddhiman Saha made way for Dhoni, who missed the first Test due to a thumb injury while paceman Umesh Yadav has replaced Mohammed Shami.
Off-spinner Ravichandran Ashwin takes place of leg-spinner Karn Sharma.
Australia will be led by young Steven Smith in the absence of injured Michael Clarke, who has been replaced by Shuan Marsh.
The hosts have also dropped Peter Siddle and Ryan Harris, bringing in Mitchell Starc and Josh Hazlewood, who will make his debut.
India: Mahendra Singh Dhoni (c) Shikhar Dhawan, Murali Vijay, Cheteshwar Pujara, Virat Kohli, Ajinkya Rahane, Rohit Sharma, R Ashwin, Ishant Sharma, Varun Aaron and Umesh Yadav.
Australia: Steven Smith (C), Chris Rogers, David Warner, Shane Watson, Shaun Marsh, Mitchell Marsh, Brad Haddin, Mitchell Johnson, Mitchell Starc, Josh Hazlewood and Nathan Lyon.