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 Group B games with Iraq bottom on five ahead of their eighth and final fixture away to Australia next week.
After losses to Jordan and Bulgaria, Japan coach Alberto Zaccheroni was keen to grab a win before the team begin their Confederations Cup campaign against hosts Brazil on Saturday.
"It's been a while since we'd won so I told the players to finish off with a victory," the Italian was quoted as saying by Kyodo news agency.
"The heat and wind made things difficult but we did well enough tonight. I think we showed we have been a force to be reckoned with in this group."
Iraq knew only victory in front of a handful of fans in their temporary home ground in Qatar would be enough to keep alive their hopes of claiming a top-three finish and a chance of reaching Brazil.
The Japanese, who sealed top spot in the group last week with a point at home to Australia, rested first-teamers Keisuke Honda, Ryoichi Maeda and Maya Yoshida for the fixture, while skipper Makoto Hasebe was suspended.
WATER BREAKS
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 (86 degrees Fahrenheit) 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, who will retire at the end of the campaign, 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.
"I was free and was going to go for it myself but made the right decision," said Endo, who captained the side in the absence of Hasebe.
"We have the Confederations Cup next and hopefully the team can perform well."
