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India won the two-match series 1-0 after they claimed the first test in Chennai by six wickets having achieved a memorable fourth innings target of 387 runs.
Tuesday's result in Mohali was the first draw under Dhoni, who began his captaincy with three wins, including the 2-0 home series win over Australia.
Dhoni said he chose to allow opener Gautam Gambhir, out for 97 after a first innings 179, and Yuvraj Singh (86) to go for their hundreds on the last day instead of setting a target.
Poor light due to fog affected all five days and Dhoni said the unpredictable weather meant he could not take any risks.
"It is not always easy," he told reporters. "There was not much wear and tear on the pitch. I was not 100 percent sure we could put them in and take the wickets.
"We were leading in the series, we didn't want to give England any chance. We were not sure about the weather, you're thinking 350 runs (target), but it can be easily achieved if 90 overs were possible."
England, set an improbable 403 runs to get in 43 overs, were 64 for one when play was called off after tea, after two-and-half hours were lost due to fog in the morning.
Dhoni praised England for their resilience and for resuming the aborted tour after last month's militant attacks in Mumbai had raised serious doubts over whether the tests would go ahead.
"It was 10 days of really good cricket," Dhoni said. "Even the first test was interesting. Even here, when our top order wickets fell, it seemed it will go for an exciting end."
Gambhir was named man-of-the-match while left-arm paceman Zaheer Khan, who bowled superbly to claim eight wickets in the batsmen-dominated series, emerged the player of the series.
The series win helped India regain the number two spot in the International Cricket Council (ICC) test rankings. However, Dhoni said playing well was more important.
"We are not considering that fact, we need to really focus on playing good cricket," he said. "The execution of our plans have been brilliant so far."
KP hails team's grit
England skipper Kevin Pietersen praised his team's grit and individual efforts despite their test series defeat in India.
"It is not bad as some defeats, we can take a lot of positives from the series," Pietersen told reporters. "I'm proud to be captain of a bunch of boys we have brought out here," he said. "All the guys have behaved as great ambassadors of the game."
England had less than ideal preparation after resuming the aborted tour of India despite safety fears following last month's militant attacks in Mumbai.
"Indian people have been magnificent, we knew they were going to be because we came back and started test match cricket," said Pietersen. "There is nothing better than performing against knowledgeable crowds with love for the game."
The visitors lost the preceding one-day series 5-0, after the last two games were called off following the attacks.
"We came here with very little preparation for the series with the red ball against such a great side," said Pietersen.
"India is playing fantastic cricket at the moment, confident and without fear, they are on top of their game especially in India.
"But we gave ourselves a good chance in Chennai, some good stuff on that Monday but Sachin Tendulkar took it away from us."
Tendulkar hit his 41st test century as India achieved a then fourth-highest final innings target of 387. It is now fifth in the all-time list.
Although the Mohali test, shifted out of Mumbai, was badly hit by poor light due to the northern Indian winter, England also owed the draw to a masterly 144 from Pietersen on the third day.
Pietersen, who took over as captain in the home series against South Africa in the summer, said the last couple of months had been difficult as a Stanford Twenty20 debacle in Antigua was followed by the one-day series rout in India.
"It has been the toughest six to eight weeks of my career so far," he said. "To score a hundred like I did meant a lot to me."