In reply to Australia's 380 all out, India put themselves in a good position with Kohli's patient 206-ball 107 and Dhoni's pacy 116-ball unbeaten 97 being the highlights.
Also notable was the magnificent half-century by Sachin Tendulkar (81).
At the break, Dhoni was holding fort with R Ashwin (3) giving him company.
India scored at a decent pace to be 263 for four at lunch, but after the break, the innings accelerated with Kohli and Dhoni breaking free against an attack that, despite asking a few questions, never looked very threatening.
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However, the breakthrough came only after Kohli and Dhoni had put on 128 runs for the fifth wicket and that too at rapid a pace.
The two were together for 26.1 overs and plundered 54 runs off the first seven overs with the new ball that was taken in the 83rd over.
Australian skipper Michael Clarke shuffled his bowling resources and even bowled himself but the home batsmen remained fluent in their stroke-making, entertaining the large Sunday crowd that turned up at the M A Chidambaram Stadium.
Trying to go over mid-on, Kohli failed to get the elevation and ended up holing out to Mitchell Starc. His superb knock included 15 fours and a six.