Iran, meanwhile stayed on course for a Russia 2018 spot after shifting Uzbekistan from the top of Group A on goal difference with a 1-0 victory in Tashkent.
Iran are also the only team in the group not to concede a goal in three matches so far, having beaten Qatar 2-0 and drawn goalless with China earlier.
But the torment continued for Qatar as they remained at the bottom after suffering their third straight defeat on Thursday.
The 2022 hosts were done in by Tottenham Hotspur's Son who extended his electric club form with the winning goal in South Korea's 3-2 triumph in Suwon.
Qatar fought bravely and they took a shock 2-1 lead into the break thanks to Hassan Al-Haydos's penalty and Sebastian Soria's goal at the end of the first half.
But Uli Stielike's men, seeking their 10th World Cup appearance, levelled through Ji Dong-Won before Son, who has scored five for Spurs already this season, curled the winner on 58 minutes.
"This is the first time in two years that we've come back to win," said the German. "This is the victory that is very important for us because it gave us confidence before going to Iran."
Qatar's new coach Jorge Fossati, who replaced the sacked Jose Daniel Carreno only last month, said he was still optimistic after his team scored their first goals of the third qualifying round.
"I'm very optimistic about the qualification," Fossati said, adding that Qatar "confronted one of the top four teams in Asia".
In Saitama, Japan needed a 95th-minute strike from substitute Hotaru Yamaguchi to down Iraq 2-1 and stay on track in Asia's final qualifying round.
But China were stunned 1-0 at home by war-ravaged Syria as they slipped to fifth in Group A, with only the top two teams reaching Russia and the third-placed side going into a play-off series.
Japan were headed for a morale-sapping draw against Iraq when Yamaguchi smashed a loose ball from a corner through a forest of legs and into the Iraqi goal.
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