Defender Maya Yoshida rose to head home four minutes into stoppage-time in rain-lashed Saitama in their opening match in the third round of regional 2014 World Cup qualifiers.
"North Korea made us work hard but it was a terrific victory," Japan coach Alberto Zaccheroni said in a pitchside interview after the late drama.
"The players battled until the end against a great wall North Korea put in front of us. They deserve credit for the way they kept hammering away. Our patience paid off."
North Korea were unfortunate to have Pak Kwang-ryong sent off seven minutes from time for a studs-up tackle on Yasuhito Endo and the dismissal triggered a late Japanese onslaught.
"It wasn't the prettiest of wins," said Japan captain Makoto Hasebe. "I hope we'll give the fans a bit more fun in the next games but there are no easy World Cup qualifers."
Japan's clashes with North Korea have frequently been played against a backdrop of political tension relating to World War II, North Korea's nuclear ambitions and the kidnapping of Japanese citizens.
The Blue Samurai, unbeaten in 12 games since Italian Zaccheroni took charge last October, have also been drawn alongside Uzbekistan and Tajikistan in Group C.
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