The loss was set up on the opening day itself, when electing to bat in overcast conditions India were reduced to eight for four and were eventually bowled out for 152.
"It is important to put runs on the board. The number 7, 8, 9, 10 and 11 batsmen have masked the top-order so far in this series," Dhoni said at the post-match press conference as the match ended inside three days on Saturday.
"The win at Lord's also help camouflaged the poor form of the top-order and we couldn't question them that they are not scoring any runs. Our fifth bowler has scored more runs than our top-order batsmen," a livid Dhoni said.
While man-of-the-match Stuart Broad (6/25) was the tormentor in the first innings, it was England off-spinner Moeen Ali (4-39), who broke India's back in the second innings. Dhoni was all praise for the English bowling.
"On this wicket, England bowled very well. The first hour of the match was very crucial. The batting department has to improve and the top five to six batsmen have to get more runs. This defeat will hurt us," he said
The Indian batsmen didn't fare any better in the second innings as they were bowled out for 161 runs, this time in better batting conditions.
Getting behind a lead of 215 runs with more than two days to bat out, the Indian batting fell like a pack of cards in the final session of the third day's play.
"We don't know what was going to happen tomorrow or day after. The important thing was to play out the day today," said Dhoni commenting on the weather forecast.
The skipper said it was time that Indian batsmen start batting responsibly and convert the good starts into big ones.
"Most of the batsmen have played cricket for a long time and have enough experience to know the match conditions. So they can see that they have to play out sessions accordingly. Sixty overs is a very big target, you can only plan ahead for 3-4 overs at the maximum. That is your target and that's the spell bowlers go through as well.
"Most of the batsmen have gone through good spells, they have got starts and they are able to see off the most difficult phase. But they haven't been able to convert those starts. They need to start converting those starts," he said.
Moeen Ali was again the wrecker-in-chief for India. With 19 wickets so far in the four matches, he has now turned out to be the most successful spinner in the series, just two away from leading wicket-taker James Anderson (21).
"It is important to be positive against a spinner like him," said Dhoni, defending his side's aggressive intent against the spinner.
"He is quite a consistent bowler and he uses the drift well. We have to put pressure on him and if we do that then the fast bowlers have to bowl more. That was the strategy against him. Pujara had a tough decision but the others got good balls."
Dhoni however, was quick to praise his bowling attack, especially Ravichandran Ashwin, who not only bowled but batted well in the game as well -- Ashwin (46) was the last man standing when India surrendered.
"Ashwin has shown time and again that he can bat. And he can score runs at any position. We had to play two spinners because if we survive in the match till day four or five, then both Jadeja and Aswhin can exert pressure on the batsmen. Then two spinners come into play," he said.
"This wicket had a bit of juice in it and the bowlers bowled very well. I was able to bowl both Ashwin and Jadeja, and give them some rest, so they were fresh when they came on to bowl. And they bowled well on this pitch as it shows that whenever there is something in the pitch, our bowlers are able to take wickets and get the opposition out.
"In the last Test we were not able to do that, but here with a helpful pitch we were able to take wickets and that was something positive," he added.
But again the whole thing comes down to how poorly India batted in this match, not allowing their bowlers a sniff in the entire game.
"The first innings is very important especially outside the sub-continent. In the last two Tests we have slipped up in the first innings, particularly here. It is difficult to come back from a position like that. We need to review how we play in the first innings and how we apply going forward from here. We need to make sure that we make the first two hours of the next match count properly," Dhoni signed off.