The Blue Samurai, ranked 15th in the world, were made to work hard for their three points against a Korean side ranked a lowly 114th in the world.
In the end, Maya Yoshida broke the deadlock in the depths of second half injury time to get Japan's qualifying campaign off to a winning - if not impressive - start, and stretch Zaccheroni's unbeaten run as Japan coach to 14 games.
"I think North Korea played their 100 percent. We had to be patient, patient, patient, but we were threatening them repeatedly and finally Maya scored a goal," the Italian told reporters after the game.
"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."
Japan's goal hero Yoshida was equally delighted with the way his side kept going until the last.
"We started playing long balls more after (substitute Mike) Havenaar came on, and it was great that we got there in the end and took the three points," he said.
Japan now travel to play Uzbekistan, 1-0 winners away in Tajikistan on Friday, in Tashkent on Tuesday.