Pak Nam-Chol's 50th-minute strike proved to be the difference as Korea DPR defeated Japan 1-0 at Pyongyang's Kim Il Sung Stadium on Tuesday.
On 50 minutes Ri Kwang Chon's long ball into the box reached the head of Pak Kwang Ryong, who set it up for a Pak Nam Chol to nod in the only goal of the game, triggering an ear-splitting ovation that lasted several minutes.
North Korea had dominated Zaccheroni's youthful Japanese side with Pak Song Chol threatening from a free-kick in the 26th minute.
In the 40th minute, defender Pak Nam Chol sent over a menacing cross, but Pak Song Chol's diving header just missed.
The midfielder's goal avenged his side's September defeat in Tokyo and sparked jubilation in the seemingly capacity crowd.
But the hosts' first win in qualifying came too late to save their campaign, which was ended last week by Uzbekistan, while Asian champions Japan were already through to the last round with ten points from their first three games.
The match was an ill-tempered affair with Bahraini referee Nawaf Shukralla showing eight yellow cards to Korean players including Jong Il-Gwan, who was dismissed for his second caution on 77 minutes.
"It was a physical match in a tough environment," Japan coach Alberto Zaccheroni told Japanese broadcaster TBS.
"I suppose our opponents were also feeling pressure for this match against Japan. Their spirit might have showed in the number of yellow cards they received," he said.