A much-changed Japanese side found themselves 2-0 down after 40 minutes in Yemen but a hat-trick from substitute Sota Hirayama, finished in the 79th minute, completed a brave 3-2 comeback win and booked a place at the finals for the Blue Samurai.
Japan top Group A on 12 points from five games with Bahrain, who also went through in second place after they thrashed Hong Kong 4-0 at home, level on points in second.
"The last minutes of the first half we lost control of the midfield, but the second half we were much better organised," Australian coach Pim Verbeek told Fox Sports.
"A little bit more sharpness in one-on-one situations and we could have won the game."
Some questionable refereeing decisions overshadowed Iran's 3-1 victory over Singapore which booked their place in Qatar and eased the pressure on coach Afshin Ghotbi, who had fans handing out posters with his face crossed out before kick-off.
"I hope that everybody believes that the referee wasn't the difference," Ghotbi told reporters. "I think it was the quality of the Iranian team."
"I've seen enough of this Thai team to say that if I have everyone fit, we can do really, really well," Robson said. "Even a draw is enough. I have confidence in these players that they can do this."
China sealed their place at the finals after a 0-0 draw with Group D leaders and already qualified Syria was enough following third-placed Vietnam's 1-1 draw at bottom-side Lebanon.
In Group C the United Arab Emirates made coach Srecko Katanec's first competitive match in charge a memorable one as they scored an injury time winner to beat Malaysia 1-0 and qualify for the finals.
