A freak own goal by defender Ri Yong-Chol 25 minutes from time in Tokyo proved the difference in a tempestuous East Asian championship clash bristling with testosterone and pent-up emotion.
The result dashed any faint hopes North Korea had of winning the four-team tournament after they were sunk by a deflected late goal in a 1-0 loss to hosts Japan at the weekend.
"It was a special game for us -- special for the players and for the country," North Korea coach Jorn Andersen told reporters.
"We were unlucky to lose against Japan but I'm less satisfied today. I don't know what the whole reason is that we didn't play well."
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Studiously avoiding eye contact in the tunnel before kickoff, both sets of players belted out their national anthems with gusto before a grudge match played out against the backdrop of Pyongyang's recent missile launches and spiralling war of words with Washington.
North Korea, playing in red and cheered on by several hundred pro-Pyongyang ethnic Koreans living in Japan waving North Korean flags, tore into their cousins from south of their heavily fortified border.
But it was the South, held 2-2 by China in their opening game, who looked the likeliest to score, despite missing several key players such as Tottenham forward Son Heung-Min.
- Strained relations -
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Lee Chang-Min fired a shot just wide with the best chance of the first half, and then a snap shot from striker Jin Seon-Guk rattled the post just before the hour mark.
Relations between the two Koreas have been stretched to breaking point after the secretive North's sixth nuclear test in September, and tempers on the pitch threatened to flare on several occasions.
Jong Il-Gwan dragged a shot wide in a rare chance for North Korea five minutes later but they never seriously looked like producing an upset following a plucky performance against Japan.
Despite United Nations sanctions against North Korea over the country's nuclear weapons programme, their footballers were allowed to compete in the four-team tournament after the Japanese government waived travel restrictions.
The biennial East Asian tournament was first held in 2003 when South Korea won the first of their three titles, a year after reaching the semi-finals of the World Cup as co-hosts with Japan.
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