It had shaped up to be another disappointing occasion for the African side, who frequently flatter to deceive, when Keisuke Honda powered Japan into a first-half lead.
Yet Drogba’s introduction was swiftly followed by quickfire headed goals from Wilfried Bony and Gervinho in the space of three second-half minutes that turned the match on its head.
The victory at the Pernambuco arena moved the Ivorians level on three points at the top of Group C with Colombia, who beat Greece 3-0 earlier on Saturday.
With coaches so often judged on their ability to make brave decisions, Ivory Coast’s Sabri Lamouchi put his neck on the line by leaving out Drogba, for so long a talismanic presence in the lineup, in favour of the in-form Bony.
He claimed after the match it was partly due to the striker’s lack of fitness, but he also admitted it was a tactical decision.
It initially looked a poor call as Japan had the better of the first half, but the striker’s appearance proved decisive in wrestling the momentum towards the Africans.
Within seconds of coming on he had driven at the heart of a swiftly retreating Japanese back four, inspiring panic in the massed blue ranks that had been previously unthreatened.
“When Didier Drogba came on the pitch everything changed,” Frenchman Lamouchi told reporters. “When you have this caliber of player on the pitch you are very lucky. “Of course, he was frustrated to be on the bench but if you saw the joy when he finished the match… he is a champion.”
At 36 years old, Drogba is nearing the end of a career where he has made a habit of bullying defences into submission. Nonetheless, he had the look of a man who feels he still has unfinished business playing for his country.
While he has led them to the last two World Cups and five straight African Nations Cups, his international career has been marked by frequent and bitter disappointment, typified by the Ivorians’ failure to emerge from their group in 2006 and 2010.
This campaign had looked in danger of turning sour as well.
Japan started brightly and were sharp and nimble in possession, working clever angles as they picked off their opponents’ frequently misplaced passes and took the lead with a goal of genuine quality from Honda after 16 minutes.
Collecting a pass across the box, he took one touch to shift it out of his feet and then drove it powerfully into the top corner with his left foot, before galloping away in celebration as blue hordes of Japanese fans celebrated deliriously.
The Elephants had their moments, with midfielder Yaya Toure showing occasional glimpses of his destructive powers, shifting through the gears with trademark bursts of raw energy.
Yet there was little killer instinct as half chances came and went, with Drogba prowling on the sidelines before entering the fray after 62 minutes.
The change had the desired impact on the Ivory Coast who levelled two minutes later when Bony leapt to glance a fizzing Serge Aurier cross into the far corner.
Two minutes later and a drilled Aurier centre was met this time by Gervinho who got in front of his marker to direct a header on goal that squirmed past Japan keeper Eiji Kawashima.
Japan coach Alberto Zaccheroni felt his keeper was not the only player who could have done better.
“I expected a different performance and I want to analyse what I did and I will speak to players tomorrow,” he said.
“The day after that I will know if it is an issue of maturity or something else,” he added. “I know they can do better because they have done better many times before…
“We have two matches coming up and we have to keep the morale high. What we have done does not count that much. What counts is what we need to do.”
Japan next face Greece on Thursday when the Ivory Coast are up against Colombia.
(Reporting by Toby Davis; editing by Ken Ferris)