It came as the result of poor defending when Cameroon failed to cut out a cross from Daisuke Matsui, with Honda, who helped his club side reach the Champions League quarter-finals last season, making no mistake at the back post.
"I had to stay calm when the ball came to me as we have missed chances in recent games," he added.
Japan's cause was helped by a desperate showing from the African side.
Paul Le Guen's team struggled to create any decent chances, despite having a great deal of possession, although Japan goalkeeper Eiji Kawashima made a superb diving save to deny substitute Mohamadou Idrissou in stoppage time.
Coach Takeshi Okada allowed himself a wry smile after the game.
He said: "We knew Cameroon would be physically strong and so it proved. But my players had a strong motivation to do well.
"They asked me before the match if they could stand with shoulders linked at the national anthem. I thought it was a good idea."
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