India headed into the third match of the five-Test series at the Ageas Bowl leading 1-0 after winning at Lord's last week, but were outplayed on all five days as England made it 1-1 on Thursday.
The tourists replied to England's declaration of 569-7 in the first innings with 330 and, having been set a target of 445 for victory, India were skittled for just 178 in the second innings with Moeen Ali taking Test-best figures of 6-67.
And captain Dhoni was left frustrated with the manner in which his side wilted at key stages of the game in Southampton.
"I don't think we played good cricket early on," he said at the on-pitch presentation.
"There were quite a few soft dismissals, that phase when Jinks [Ajinkya Rahane] got out and a couple of others fell had a big impact on the game.
"And I think last night, that last session had a big impact. We lost a few wickets and a few of them were soft dismissals. Without that session we would have been facing a different game."
Ali did the damage for England on the final day by taking four wickets to add to his two on Thursday and Dhoni was disappointed with the way the tourists played the off-spinning all-rounder.
"I think we played the fast bowlers well, Moeen bowled well but we let him bowl well," he added "It's important to be positive against spinners."
In a further blow, Dhoni revealed that injured pace bowler Ishant Sharma would still be unavailable for the fourth Test which starts at Old Trafford on August 7.