Japan's AC Milan star Keisuke Honda knocked the Elephants groggy with a 16th minute goal to make it 1-0.
But goals from Wilfried Bony and Gervinho in the 64th and 66th minutes saw Ivory Coast home.
Honda gave Japan hope after escaping his markers at the edge of the penalty area and firing home a left foot shot that gave Boubacar Barry Copa in the Ivory Coast goal no chance.
Ivory Coast had chances but never looked confident and had more scares after the goal. Copa was lucky that Atsuto Uchida fired a 24th minute shot straight at him.
Japan's English Premier League defender Maya Yoshida was booked for a clumsy tackle that stopped Serey Die getting a shot at goal from just outside the penalty area. Yaya Toure's shot from the free kick went over the bar.
Honda was unlucky not to get a second goal in the 36th minute when his deflected shot flew over the bar.
Veteran striker Didier Drogba came on for Die Serey after 62 minutes and was immediately in the thick of the action as Japan resisted waves of attacks.
Two minutes later Bony headed past Japan's floundering goalkeeper Eiji Kawashima.
Less than two minutes later, the Elephants erupted in rapture when Gervinho headed past Kawashima into the opposite corner. (AFP)