Chasing India's total of 271 for eight, England were well on course in the fifth and final ODI but collapsed embarrassingly from 129 without loss to 176 all out.
"We were in with a shout at 120-odd for nought and just got blown away at the end. It was very disappointing," said Cook, whose side lost the match by 95 runs.
"We know you can lose wickets in clusters and we seem to have lost 10 there in a cluster.
"We set up the game beautifully to go on and win that, but credit to the way they bowled and we played a couple of poor shots. It was a bit of a disappointing end and a bit of a common theme."
MS Dhoni, the India captain, made 75 not out with some vital late hitting to boost his side's total and was not dismissed throughout the series.
Cook added on Sky Sports 1: "Credit to MS, at the end he hits it very well, he's a very hard person to bowl at and he single-handedly got them up to 270, which was probably gettable the way we started.
"But when you lose 10 for 50 you're not going to win anything.
"Only four of us have played one-day series out here and it's great for the youngsters to get the experience. It will show where they need to improve and we all need to improve as a side.
"We got thoroughly beaten out here but there are quite a few positives, I thought Steven Finn throughout the series has been excellent.
"It's always hard when you lose 5-0 but there are always positives to take from it."
Dhoni said: "It was a very ugly looking wicket and one ball can swing or keep low. It was very difficult to score on so we were fortunate to score 270. 240 or 245 was in our mind and then wait for the wicket to spin.
"I want to stay to the end [of the innings] and whatever is in my area I look to hit it over the boundary.
"It's important to see which bowlers are left and who you can target. After that it's about who can bear the pressure well. I love to stay to the end and I've been supported by the other batsmen."
The tourists appeared to give themselves an obvious chance of breaking their one-day international duck at the last attempt on this nightmare tour when they coasted to 129 without loss in little more than 20 overs.
But then Ravindra Jadeja (four for 33) and the India attack conspired to undermine England's batting once Varun Aaron, the young fast bowler, had ended a highly promising stand between Craig Kieswetter and Cook.
Five wickets fell for 12 runs in 35 balls - and soon afterwards all 10 for 47 - as India's slow bowlers found telling turn which had been conspicuously beyond Graeme Swann and Samit Patel (three for 57).
Cook (60) and Kieswetter (63) crashed 17 fours - and a six for the latter - as they tucked into India's seamers, and then consolidated initially with the pace off in near run-a-ball half-centuries.
But Aaron bowled Cook off his pad with a quick delivery which kept low, and then came the capitulation to spin.
Kieswetter pushed forward defensively but did not use his bat against Jadeja; Ian Bell, playing for the first time in the series because of the thumb Kevin Pietersen broke in Sunday's Mumbai defeat, nicked behind a doosra from R Ashwin (three for 28); and Jonathan Trott edged the slow left-armer to slip.
The terminal damage continued when Jonny Bairstow tried to hit against Jadeja's spin and was caught at point.
With that there was simply no way back for England as their collapse duly careered further out of control.