The hosts wrapped up the series 2-0 when they dismissed Australia for 209 in its second innings, Harbhajan Singh snaring the final wicket of Mitchell Johnson, who was trapped LBW for 11.
Australia, set a target of 382 for victory, folded up for 209 runs to give India the Border-Gavaskar Trophy. India thus gave a fitting send off to Sourav Ganguly for whom this was his last Test.
He was today given the honour of leading out the Indian team in the morning for the last time in his career.
Resuming from the score of 111 for three at lunch, Australia needed Matthew Hayden and Michael Hussey to play for as long as possible if they would be thinking of even saving the Test let alone win it.
Hayden seemed to be in a hurry with Dhoni employing a leg side field after lunch with as many as five fielders on the boundary line saving the fours.
However, Hayden still managed to find the boundaries reaching his 50 in the first over after lunch hoicking Virender Sehwag to the long on fence.
Hayden made his half century in 73 balls with five boundaries.
He then took on Harbhajan Singh piercing the leg side beautifully for two consecutive boundaries and then lofted Sehwag for a huge six over long on.
At the other end, Hussey was using the reverse sweep to good effect as the Australians kept up the scoring rate which saw some sort of panic in the Indian camp.
However, Dhoni, who now has won all the three Tests he has captained, produced a masterstroke bringing on leg spinner Amit Mishra for Harbhajan Singh. Mishra removed the in-form batsman of the series Hussey with a peach of a delivery which straightened and bounced as the left hander went forward to play a defensive shot.
The ball took the top of the bat and flew to Rahul Dravid at first slip who made no mistake.
Hussey made 19 and had put on 68 runs with Hayden for the fourth wicket.
Four runs later, Matthew Hayden was also back in the pavilion and with it any chances of Australia making a match of it evaporated.
Hayden tried to pull Harbhajan but missed the ball completely which wrapped him on the pads right in front of the wicket.
Hayden made 77 after facing 93 balls which also included eight boundaries and a six to leave Australia reeling at 154 for five with the top order back in the hut.
The spinners then applied the pressure on the lower order which caved in with Amit Mishra taking three wickets and Harbhajan ending up with four wickets in the innings as Australia folded up for 209 to give India the victory.
The Australians, however, had something to smile about the debut off spinner Jason Krejza who grabbed 12 wickets to become the fourth best bowler on debut in terms of wickets, winning the man of the match award.
Ishant Sharma won the man of the series award.