The Blue Samurai, ranked 15th in the world, could do no better than a hard-fought 1-0 victory against the 114th ranked Korean side at the Saitama Stadium.
Their blushes were saved by Maya Yoshida, who scored in the 90th minute.
The Koreans were resolute in defence, but Japan were also handicapped by the loss of Keisuke Honda, Kengo Nakamura, and Yuto Nagotomo to injury, and will thank their lucky stars for the continuation of an unbeaten run under Alberto Zaccheroni that has stretched to 14 games.
The loss of the dynamic trio showed for the reigning Asian champions, who struggled to make the breakthrough until Park Kwang-Ryong was given his marching orders for a high challenge, leaving Korea DPR to struggle with just ten men.
Japan were unlucky not to take the lead earlier, as newly capped Mike Havenaar, a naturalised citizen as a result of his Dutch parents who emigrated to Japan, hit the bar just five minutes after coming on in the 69th minute.