Indian captain Dhoni told reporters that it was wrong to see the win as "revenge".
In a cricket-addicted nation, Dhoni was taking his first cricketing steps at a late stage.
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Harbhajan and Mahendra (Dhoni) played very well last night and we probably missed an opportunity there.
But Dhoni has been named in the squad for the 50-over tournament in Pakistan in September.
Dinesh Karthik and Parthiv Patel will compete for vice-captain Dhoni's place behind the stumps.
Dr Dhoni - the honorific thanks to a university in Leicester - is 30.
After lunch Dhoni played a series of strokes seldom witnessed at the famous old London ground.
In another high quality piece of late action, Dhoni was caught brilliantly in the deep by Bray diving forward.
India captain Dhoni paid tribute to his fast bowlers Ishant Sharma and Zaheer Khan after the win.
Tendulkar is hurt after the first game, and Sehwag and Dhoni, two big hitters, haven't fired yet.
Dhoni, 28, will be unavailable for the matches in Cuttack and Kolkata on 21 and 24 December.
Earlier, Dravid, Mahendra Dhoni and Irfan Pathan were all out caught at point or gully after loose cuts.
But the fourth-wicket pairing of Dhoni and Kohli produced 152 runs and changed the course of the game.
Dinesh Karthik, Mahendra Dhoni and VVS Laxman were all dismissed cheaply for the second time in the game.
Dhoni said uncertainty about whether fog would delay the start of the final day had influenced his decision.
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Dhoni received excellent support from Rahul Dravid, who was content to give his partner most of the strike.
Tamil Nadu opening batsman Murali Vijay is the only newcomer in a 15-man squad captained by Mahendra Dhoni.
After winning the toss, India skipper Mahendra Dhoni decided to bat first in front of thousands of passionate fans.
Zaheer rounded off the innings when last man Peter George gloved a short delivery through to wicketkeeper Mahendra Dhoni.
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Dhoni says the shift from his football obsession came in the 1994-95 season.
BBC: SPORT | Cricket | International Teams | India | Dashing Dhoni's chance discovery
"It was a very interesting series and it's good to come from behind, " said India captain Mahendra Singh Dhoni.
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This left Dhoni to put on 94 for the fifth wicket with Raina.
Virender Sehwag's dazzling 64 off 36 balls and Mahendra Dhoni (46 off 28) gave the hosts the perfect platform.
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At Dominica in the West Indies, Dhoni emerged as the most defensive of captains, unwilling to take calculated risks.
"We need to be patient because it's a flat wicket and there are good batsmen still to come, " said Dhoni.
Dhoni declared immediately, giving his bowlers a session and a half to claim an unlikely victory by bowling England out.
But now, the promotion of Pathan, Dhoni and Yadav in the batting order has been part of a planned strategy.
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Earlier Yuvraj Singh struck 77 and Mahendra Dhoni hit two sixes in 51 from 51 balls as India declared on 375-6.
Youvraj and Dhoni could only sit helplessly on the boundary edge as Jadeja struggled to keep up with the scoring rate.
Having batted so poorly against South Africa, and been put into bat by Dhoni, it was crucial that England started positively.
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