At the break, India had progressed to 404 runs for five wickets with Sourav Ganguly, playing his last Test match, unbeaten on 80 while Dhoni was batting on 43 runs.
India is one up in the four-match series and Australia need to win this Test to square the series and retain the Border-Gavaskar trophy.
Resuming on 311 for five, India started off confidently with Ganguly essaying a late cut off Jason Krejza in the first over itself to get the home team going.
However, in the same over, the hosts nearly lost a wicket when Dhoni tried to straight drive Krejza only to get an inside edge which bounced near his boot and went back to the bowler, who claimed the catch.
The umpires Aleem Dar and Billy Bowden, after consultatind each other, gave Dhoni not out.
This was the only time when the Aussies came close to taking a wicket as Dhoni and Ganguly did not give even an iota of a chance to the bowlers.
Dhoni and Ganguly kept the scoreboard moving by cleverly placing the ball into the gaps and running hard between the wickets picking up twos and threes as the score kept on swelling.
Dhoni, showing his intent from the very beginning, flicked Brett Lee to the square leg boundary for a four and then Ganguly essayed a classical square cut off Mitchell Johnson to the point boundary.
Krejza, who was given the opening over from the pavilion end was then brought on from the far end from where he had got his wickets yesterday. He was immediately given the treatment by Sourav Ganguly who stepped down the track to loft him over long on for a huge six.
The south paw then reached his 35th Test half century in his last Test by pusing Kreja to long off fora two runs. Ganguly reached the landmark after facing 95 balls and his innings was studded with four boundaries and a six.
He celebrated his reaching the landmark by stepping down and lofting the bowler over mid-off for a boundary. This forced Krejza to adopt a defensive line for the first time in the match and he started bowling outside the leg stump of the left hander who was more than happy to pad the deliveries away.
Ganguly, however, did not allow Krejza to settle into a negative line and swept him to the square leg boundary to break the shackles.
The Kolkata batsman then shaped to cut Krejza who changed his line to middle and off stump and the ball flew past Matthew Hayden at first slip for another boundary which brought up the 100 runs partnership between the two which came in 29.3 overs.
At the other end Shane Watson managed to keep Dhoni quite with a nagging line and length as both the batsmen started playing for lunch, not taking any risks with India in the driver's seat.
Ganguly, who is on 80 will become only the second Indian if he reaches the three figure mark to make centuries in his debut as well as last Test match. Mohammad Azharuddin is the other Indian to have done so.