After being reduced to 34/4, India were bowled out for 146 in 35.1 overs, chasing 281 runs in the second one-dayer. No batsman crossed the 40-run mark.
"In the last few series our middle order, to some extent, was a bit of a bother. In this series we lost the top three quite early and our middle order was exposed. So if you assess, then that's maybe why we haven't been able to perform to our potential," he said.
Dhoni said he was surprised that Indian batsmen could not take advantage of a flat track.
"The wicket was on the flatter side and there wasn't much for the fast bowlers in it, so I am disappointed with the batting. The kind of shots we played, well, few of them were on. But the shot execution was not great to some extent, as they went to the fielders," he said.
Dhoni though expressed his pleasure about the bowlers' performance.
"Compared to the last game, our bowling did a fantastic job especially in the middle orders. Spinners bowled well and so did the fast bowlers when they came back on, in the latter stages of the South African innings. I am happy with the bowlers' performance because 280 runs on this pitch was a decent score."
South Africa were put into bat by Dhoni and while his bowlers eventually finished on top, early on they were once again defied by Quinton de Kock and Hashim Amla, with the opening duo putting up 194 runs for the first wicket and smacking a hundred each in doing so.
"They have done really well for South Africa. They did so in the last series as well (versus Pakistan). The way they were batting in the first 20 overs, I thought this may be another 300-plus run chase but we came back into the game.
Dhoni said South Africa have good combination in both batting and bowling and that has played a major role in their continuing success.
"In both matches in this series so far, they have done well and given a really good start, but in this game we were able to get to the middle order to some extent because they were not able to score 300-plus runs. At the moment, South Africa have the right kind of bowlers and the right batsmen."
To counter them, Dhoni had deployed spinners as early as the 11th over, and brought on Suresh Raina and Virat Kohli as well. This turned out to be a ploy in the end, as he was able to use his bowling attack more effectively in the later stages of the South African innings.
"The wicket was slowing a bit. So, using the part-timers gives me a few more overs of specialist bowlers a bit later on," said the skipper, explaining his move.
"It seemed at that time that the batsmen were not really looking for the big strokes and I thought I can get a few overs off the part timers and then look to attack with the spinners. Or use the pace bowlers, if the pacers go for runs."
"To some extent I didn't need them (spinners) in the last few overs because fast bowlers did well apart from the couple of overs that went for runs. So, overall as a bowling unit I think we bowled well," he added.
Standing apart from the bowling unit, and indeed the entire team, was Mohammad Shami. He took 3 for 48 here at Durban, to go along with 3 for 68 in the first ODI. And Dhoni deemed him the one big positive of the tour so far.
"He bowls with the seam upright and he bowls the right line and length. Even today (Sunday) when there was a bit of reverse swing he bowled the right length, and that's something very crucial. I think he has adapted very well. And the more he is playing the better he is getting, so that's a big positive for us," said the skipper.
While the bowling may have worked on this day, owing to a slower pitch than in Johannesburg, it cannot be denied that 281 was a gettable target.
Even so, Dhoni looked to defend his batsmen and said that team India will be looking to 'continue playing their best XI' in the third ODI at Centurion on Wednesday, rather than experiment or give other squad members a chance in the dead encounter.
"When we travel outside India, people talk about short bowling because in the subcontinent we are not used to that kind of bowling. So what we have seen is that sometimes you play a few shots and it pays off, then the opposition has to think where they need to bowl.
"This is what happens in the Champions Trophy. At other times, you play those big shots and end up losing wickets. It is a part and parcel of the cricket and we will have to accept it," he opined.
The Men in Blue may have won in England back in the summer, but it will quickly become a distant memory if the tour continues to go this way. Yet, Dhoni sounded confident that this ODI series is a 'one-off contest' and there is much to learn ahead.
"You win a few and you lose a few. What's important is that you keep learning. The bowlers learnt from the first game and bowled better in this game. As a batting unit also, we need to learn quite a few things and keep going onto the field," he signed off.