His bright start to life as England captain at the end of 2012 now appears like a dim and distant memory as Dhoni carried on a trend started by Australia's Michael Clarke before handing the baton on to Sri Lanka's Angelo Mathews.
Cook's poor form and questionable leadership have come under intense scrutiny with some critics suggesting he should give up his place at the top of England's batting order and take a break from the game following Monday's painful 95-run defeat.
The England skipper has little time to rally his troops ahead of the third test starting in Southampton on Sunday, needing to lift his underperforming senior players and without the services of injured wicketkeeper Matt Prior for the rest of the series.
Cook's malaise began with the 5-0 Ashes rout in Australia, continued when a modest Sri Lanka eked out a 1-0 series win in England earlier this summer and was amplified by being forced to eat humble pie by an average Indian attack in his own backyard.
The gravity of the latest defeat gains even more perspective when it was carried out by a notoriously poor-travelling India side that had not tasted an away test victory since beating West Indies at Kingston in 2011.
Cook's captaincy in the Lord's test provided further ammunition to detractors like Shane Warne, a constant critic of the Essex player's "negative and boring" leadership.
England baffled the fans and pundits alike when Cook asked India to bat first at Lord's on a greenish wicket and their pacemen proceeded to dish out a barrage of ineffective bouncers in the first session of the test.
Similarly surprising was Cook's decision to spread the field for India's number 10 batsman Mohammad Shami, that too when his premier bowler James Anderson had the second new ball in his hand.
However, those frailties pale in comparison to how one-by-one his batsman succumbed to India's hook trap after lunch on the final day, bounced out with an old ball by an erratic Ishant Sharma, who needed to be goaded into bowling short by Dhoni.
"He's not scored a hundred in 27 innings, tactically he's been all at sea for a while now," former England captain Michael Vaughan told BBC, summing up Cook's situation.
The often outspoken former opener Geoffrey Boycott was even harsher in his assessment.
"Only Alastair Cook, his wife and family want him to remain as captain - nobody else," he said.
Cook's lack of tactical nous at Lord's stands in stark contrast to the way Dhoni marshalled his team so skilfully, with the Indian skipper also going into the match under considerable pressure.
Regularly poor away from the sub-continent, India entered the contest with a 15-match winless streak in overseas tests leaving critics like Ian Chappell believing it was time for Dhoni to hand the reins over to a new driver.
The 33-year-old from Ranchi, however, sniffed a rare opportunity against an English side still smarting from the Ashes rout in Australia and an aftermath that prompted wholesale changes to the composition of the test squad.
Dhoni set attacking and innovative fields, smartly rotated his bowlers and then came up with a masterstroke on the final day when he asked a reluctant Sharma to target the confidence-sapped Englishmen with a battery of bouncers.
"To start with it was a bit difficult to convince him, so the last two overs when he came in, I just told him to bowl short," Dhoni told reporters after the victory.
"I set a field to him so that he doesn't even think of bowling up, so that was the strategy - give him a field where he is forced to bowl the kind of length I want him to bowl."
Sharma, whose seven second innings wickets earned him the man-of-the-match award, was naturally effusive in his praise for his astute captain who persisted with the old ball.
"...with the new ball the batsman can judge the bounce with ease, while with the old one he cannot gauge the bounce as some might take off and an odd one will keep low," Sharma told www.bcci.tv.
"I feel all the wickets I got today should go to MS bhai (brother) because he planned them and set the field for them."