* Forwards Bony and Gervinho on target for Ivorians
* Drogba comes off the bench to help turn the tide
* Japan fail to hold lead from early Honda strike
The African side trailed to a stunning Keisuke Honda strike in the first half, but the introduction of forward Didier Drogba off the bench proved the catalyst to turn the match on its head after the restart as they scored twice in three minutes.
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.
It looked a poor call as Japan had the better of the first half, but the striker's appearance in the second half proved decisive in wrestling the momentum towards the Africans.
"When Didier Drogba came on the pitch everything changed," Frenchman Lamouchi told reporters. "When you have this calibre 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."
Japan started brightly. They 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.