An entertaining match was settled by an own goal from Akmal Shorakhmedov just before half-time, the Uzbek defender heading Kim Young-gwon's cross from the right past his helpless goalkeeper.
The Koreans had the better chances on a slick surface in Seoul on Tuesday with towering striker Kim Shin-wook causing the visitors numerous problems in the air.
A flicked header by the forward gave Asian player of the year Lee Keun-ho a fantastic chance to open the scoring in the 11th minute but the tricky forward sliced his shot hopelessly wide from six metres.
The Uzbeks also played well although they struggled in the final third, striker Ulugbek Bakayev offering their best chance with a fizzing shot from distance that was palmed away.
The Koreans always looked more likely to score and they took the lead three minutes before half-time when Kim Young-gwon cut inside on to his left foot and his inswinging cross was flicked in by Shorakhmedov at the near post.
The Uzbeks, who are at home to Qatar in their final match next Tuesday, took the game to the Koreans in the second half.
They threw on substitute forwards Aleksandr Geynrikh and Sanzhar Tursunov but were still unable to create clear-cut chances.
The Koreans comfortably held out for the three points which left them on the verge of their eighth consecutive World Cup finals appearance.
Iraq enjoyed plenty of possession and created lots of chances in the searing Qatari heat but could not find a way through and Japan made them pay with an 89th minute goal on the counter from Shinji Okazaki.
The result leaves Japan on 17 points from their eight games with Iraq bottom on five ahead of their eighth and final fixture away to Australia next week.
Iraq knew only victory in front of a handful of fans in their temporary home ground in Qatar would be enough to keep their hopes of claiming a top three finish and a chance of reaching Brazil alive.
The Japanese, who sealed top spot in Group B last week with a point at home to Australia, rested first teamers Keisuke Honda, Ryoichi Maeda and Maya Yoshida for the fixture with an eye on their Confederations Cup opener against Brazil on Saturday in Brasilia.
Despite the absentees, the Japanese came close to the first goal with striker Mike Havenaar narrowly missing with a glancing header in the 32nd minute and Yasuyuki Konno blazing over a good opportunity from close range four minutes later.
The game was then stopped for the first of two water breaks with the temperatures over 30 degrees Celsius in the country which will host the 2022 World Cup finals.
Iraq, 2007 Asian champions, were better suited to the heat and wrestled control of the match in the second period with captain Younis Mahmoud looking dangerous in attack.
Forward Alaa Abdul-Zahra wasted a good chance to give Iraq the lead in the 69th minute after he took advantage of some careless Japanese defending but he fired his shot over the bar.
Iraq's hopes of finding the necessary win were then hurt by two quick yellow cards that led to Alaa's dismissal in the 82 minute after he received the second for kicking an opponent in the face when attempting an overhead kick.
Despite being reduced to 10 men, Iraq piled forward in the closing stages but Japan caught them on a swift counter with midfielder Yasuhito Endo selflessly squaring the ball for Okazaki to slide home a winner in the final minute.
In the late game, Iran thrashed Lebanon 4-0 in Tehran to move into second place in Asia qualifying Group A and take control of their World Cup destiny.
Goals by Mohammad Khalatbari, Reza Ghoochannejhad and two from captain Javad Nekonam helped Iran move past Uzbekistan into the automatic qualifying places ahead of their final match away to South Korea next Tuesday.
The top two sides are guaranteed a place in Brazil with the third placed team also joining them if they can successfully negotiate a play-off against another Asian country and then a South American nation.
The Uzbeks host Qatar in their final game on Tuesday but Iran will be confident of edging them after finally finding their feet in front of goal with a dominant display against bottom side Lebanon.
- Sports & Recreation