Shinji Okazaki snatched a winner a minute from the end to move Japan eight points clear of their nearest rivals in Group B of the Asian qualifiers.
The Blue Samurai had led through Hiroshi Kiyotake's first ever international goal on 20 minutes but the hosts hit back when Ahmed Mubarak smashed in a free-kick on 77 minutes.
Japan, who were without injured Manchester United midfielder Shinji Kagawa, had the final say when Okazaki netted from close range meaning Alberto Zaccheroni's side will book their place in Brazil should they beat bottom-placed Jordan in their next game.
The Jordanians have, however, already beaten second-placed Australia at home in qualifying but their bid suffered a setback with a 1-0 loss against Iraq in Doha today [Wednesday].
Hammadi Ahmed netted in the 86th minute to grab victory and move Iraq level with the Socceroos, who were not in qualifying action today [Wednesday], and Oman on five points.
Uzbekistan, who have never qualified for a World Cup finals, went to the top of a congested Group A with a surprise 1-0 success over Iran in Tehran.
The central Asian country are a point clear of three teams with two games remaining after Ulugbek Bakaev turned in Server Djepararov's 71st-minute free-kick.
Defeat left Iran locked with South Korea, who have a game in hand, and Qatar, who edged Lebanon 1-0.
Andres Quintana netted a 75th-minute winner for Qatar, hosts for the 2022 World Cup, to keep them firmly in the hunt to reach Brazil.
Wednesday's World Cup Asian Qualifier Results
Oman 1-2 Japan
Iraq 1-0 Jordan
Qatar 1-0 Lebanon
Iran 0-1 Uzbekistan
The top two teams in each group progress directly to the World Cup finals with the third-placed teams forced into a two-legged play-off.