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The AC Milan playmaker smashed past goalkeeper Boubacar Barry on 16 minutes to give the Blue Samurai an advantage at the halfway point in their Group C opener.
Boosted by the news that Yaya Toure was fit to participate, the Elephants started the brighter of both sides and nearly took a sixth-minute lead through Wilfried Bony, whose effort deflected narrowly wide.
Japan slowly grew into the clash and saw their improvement rewarded shortly after the 15-minute mark, as Honda's fiercely-struck shot left Barry with no chance.
It could, and perhaps should, have been two just minutes later as wing-back Atsuto Uchida fended off two challenges but fired straight at Barry.
Toure fizzed a free kick narrowly over the bar but it was to be as close as Ivory Coast came to an equaliser in the first half.