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 top-two teams from each group qualify for the finals in Qatar next year.
Australia were on course to join them after racing into a 2-0 lead in Kuwait after goals from Luke Wilkshire and Dean Heffernan in the first five minutes but substitute Addul Aziz Al Enezi and Yousuf Nasser struck before halftime to deny the Socceroos in a 2-2 draw.
"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."
Kuwait lead Group B on eight points from five games, ahead of Australia courtesy of a better head-to-head record with Oman, who beat Indonesia 2-1 in Jakarta, third on seven.
A point for Kuwait in their final match in Muscat against Oman in March will book their place in the finals with Australia also needing just a point at home to Indonesia, who are out of contention.
EASE PRESSURE
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."
Group E winners Iran have 10 points from five games with the race for the runners-up spot wide-open after Thailand and Jordan played out a 0-0 draw in rain-soaked Bangkok.
One point separates the three remaining teams in the group with Thai coach Bryan Robson, the former England and Manchester United captain, confident his team can go to Iran and get the result they need in March.
"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.
