An 89th minute strike from Shinji Okazaki helped Japan beat Oman and move to the brink of qualification, while Hammadi Ahmed's goal four minutes from time gave Iraq the points against Jordan.
Hiroshi Kiyotake gave Alberto Zaccheroni's side the lead in the 20th minute with his first international goal.
Ahmed Mubarak looked to have secured a point for the hosts when his low 77th minute free-kick beat Japan 'keeper Eiji Kawashima via a deflection.
However, Okazaki's close range finish from Endo's teasing left-wing cross in the last minute of regulation time ensured the Blue Samurai go eight points clear at the top of Group B.
They will book their place in Brazil 2014 should they beat bottom-placed Jordan in their next game.
Meanwhile, Iraq grabbed their first victory of the campaign with a slender victory over basement boys Jordan in the Grand Hamad Stadium in Doha.
Hammadi Ahmed was the hero, his 86th minute strike from the edge of the area swerving beyond Amer Sabbah and into the top corner.
The victory moves Iraq onto five points in Group B, level with Oman and Australia, though the latter have a game in hand on all their opponents in the group.
Ubekistan climbed into the top spot in Group A with a 1-0 victory over Iran at the Azadi Stadium in Tehran.
Ulugbek Bakayev scored the winner to put his side in pole position with eight points.
The forward poked home Server Djeparov's brilliant free kick in the 71st minute, denting the hosts' chances of a place in Brazil.
Qatar left Lebanon bottom of Group A as they won 1-0 at home thanks to Sebastian Soria's 75th-minute goal.