Ao Tanaka's strike at the National Stadium in Tokyo gave the hosts three wins from three group B games.
The midfielder fired home from inside a crowded penalty area after a Ritsu Doan pullback.
North Korea, cheered on by a small pocket of red-shirted fans, lacked attacking power to get back in the game.
With just three points from the first three group games, North Korea need a result on Tuesday against the same opponents in Pyongyang.
The Japanese have nine points and lead Syria by five points after Hector Cuper's outfit were held to a 1-1 draw in Myanmar.
"We wanted to give our fans a good result and we are sorry we could not, but it was a good game," North Korea coach Sin Yong Nam said.
South Korea were held by Thailand to 1-1 in Seoul in their first game since Jurgen Klinsmann was fired as the coach in February after their Asian Cup semi-final defeat.
Son Heung-min put South Korea ahead after 42 minutes with a shot from close range, but just after an hour, Suphanat Mueanta levelled.
Despite dropping two points, South Korea remain on top of group C by three points from Thailand at the halfway point after China were held to a 2-2 draw by Singapore.
Wu Lei scored twice for China as new coach Branko Ivankovic made his debut in the dugout, but Singapore fought back with goals from Faris Ramli and Jacob Mahler to claim their first point in the group.
In Jordan's first action since losing the Asian Cup final to Qatar in February, they beat Pakistan 3-0.
Australia have now won all three of their Group I games after defeating Lebanon 2-0 in Sydney.
Kyrgyzstan sealed a 2-0 win over Taiwan in group D despite playing 66 minutes with 10 men due to Said Datsiev's sending off for a second yellow card while Indonesia defeated Vietnam 1-0 in Jakarta in group F.
Eldor Shomurodov gave Uzbekistan the lead in their 2-0 win over hosts Hong Kong in group E as Srecko Katanec's team moved three points ahead of Iran, who face Turkmenistan later on Thursday.
The top two teams from each of the nine groups will advance to the final round. Asia's automatic allocation at the World Cup has increased from four to eight.
With Reuters
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