Dhoni smashed 22 fours and five sixes with his knock taking just 243 balls as India finished 515 for eight, 135 ahead of Australia's first-innings effort of 380 all out.
Virat Kohli made 107 while Sachin Tendulkar could only add 10 to his overnight score of 71 on a day when Australia toiled in the field.
Australia made the ideal start when their only frontline spinner, Nathan Lyon, bowled Tendulkar through the gate.
His dismissal after a 10-over period of low scoring and disciplined bowling brought in Dhoni, whose arrival prompted an increase in the run rate as he and Kohli took to the visiting bowling attack.
Kohli launched a Lyon delivery into the stands in the 68th over before Dhoni found the ropes twice off the same bowler in the 72nd.
Moises Henriques was next to get the treatment as Kohli hit a short wide one through the covers to the boundary before cutting through the slips for another four two balls later.
India looked to continue the momentum gained towards the end of the first session, when Dhoni in particular pummelled the visiting attack.
A long hop from Clarke just after the interval was dispatched to the mid-wicket boundary by Kohli and the pair hit boundaries in the next five consecutive overs with Dhoni hitting three off Mitchell Starc in the 88th, the highlight being the first when the skipper punched a short delivery through the covers.
Kohli brought up his century and the India 300 in the next over with his 14th boundary - hitting James Pattinson through square leg to the fence.
A length delivery from Henriques was hit for a maximum by Dhoni the next over with a similar delivery two balls later going for four.
With Dhoni hitting the ball to all parts, Kohli was keen to match his skipper - but it led to his downfall in the next over.
When on 107, Kohli failed to get the elevation required to beat Starc at mid-on with the bowler taking a simple catch off Lyon to leave India 324 for five.
Dhoni attempted to maintain the impressive run rate, hitting boundaries off Siddle then Lyon, but there were a lack of runs from the other end.
There was little surprise when Ravindra Jadeja left a Pattinson delivery which clattered into off stump to and end a 44-ball, 16-run innings.
Dhoni resumed the final session on 97 not out and quickly brought up his ton, lofting Peter Siddle for four over square leg.
Ravichandran Ashwin went for three before Henriques bowled Harbhajan Singh (11) when the spinner missed an attempted slog across the line.
But with Bhuvneshwar Kumar (16no) happy to give the strike to Dhoni, the captain stepped into overdrive.
He punished anything full or short, stepping up the aggression and unsettled the Australians, who regularly changed their bowlers to little effect.
Lyon came in for particular punishment and Starc and Siddle toiled away without luck, while skipper Clarke and David Warner failed to make inroads.
As the day approached an end, all interest surrounded Dhoni's audacious bid for 200 runs in one day of Test cricket.
And he achieved the milestone with a nudge to third man off the bowling of Lyon, with the risky single - which came with less than four overs left - bringing the crowd to their feet.
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