At the tea break, Simon Katich on 18 and Ricky Ponting (7) were at the crease still 398 runs adrift of India's score with nine wickets in hand.
After Jason Krejza had seen that India were restricted below 450, Hayden and Simon Katich began the Australian innings on a positive note even as Indian captain gave the new ball to spinner Harbhajan Singh and with Zaheer Khan.
With the score at 32, Hayden (16) drove Zaheer to mid-on and set off for a run. M Vijay threw down the stumps with a direct hit with Hayden still short of his crease to give India a big breakthrough.
Earlier, India resuming on 404 for five from lunch came into a charged up Jason Krejza who took five wickets in a 26-ball spell giving away only 16 runs to hasten India's innings end.
Sourav Ganguly and Dhoni were both going strong and did not look like getting out at all.
However, Dhoni after reaching his 50 with two consecutive spanking boundaries of Mitchell Johnson, was dismissed in the next over by Krejza.
Krejza got the ball to turn from middle stump to take the leg as Dhoni played for the straighter ball and was beaten all ends up.
Dhoni made 56 in 97 balls and his innings was studded with four boundaries.
India at that time was at 422 for six. Ganguly and Dhoni added 119 runs for the sixth wicket in 204 balls to put India into a position of strength.
Two balls later, Ganguly, who had played grittily in the morning session, was deceived by a brilliant off spinner from Krejza as the ball took the edge of his bat and Michael Clarke completed a very smart catch at first slip.
Ganguly, playing his last Test match was dimissed for 85 and thus lost out on entering the list of players who have scored hundreds in their first as well as last match.
Krejza then ran through the tail and was on a hat-trick at one time after dismissing Zaheer Khan and Amit Mishra, both bowled, of consecutive deliveries.
However, Ishant Sharma denied him the hat-trick but soon was out caught by Simon Katich at forward short leg to end the Indian innings at 441, which was way short of what the hosts might have thought will be their score at lunch.
Earlier in the morning at 311 for five, India began confidently with Ganguly essaying a late cut of 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 from his boot went back to the bowler, who claimed the catch.
The umpires Aleem Dar and Billy Bowden after consultating each other gave Dhoni not out.
This was the only time when the Aussies came close to taking a wicket, as Dhoni and Ganguly then 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 beginning, flicked Brett Lee to the square leg boundary for a four and then Ganguly essayed a classical square cut of Mitchell to the point boundary.