Celtic ace Shunsuke Nakamura scored the only goal in Saitama to claim full points for the home side.
Japan are now top of the group with 11 points three ahead of Australia, while Bahrain are level on four points with Uzbekistan and Qatar.
In Tashkent, Uzbekistan spanked Hussein Yasser's Qatar 4-0 to revive their hopes of qualifying.
Farhod Tadjiyev scored a hat-trick for Uzbekistan, before Anvarjon Soliev completed the rout later on.
Ahli striker Yasser started for the Qataris, who are now bottom of the group with a negative-eight goal difference.
Uzbekistan, Bahrain and Qatar now fight for a third place spot, as Japan and Australia are almost guaranteed a place in South Africa.
Third-placed teams in both groups face each other and the winners meet Oceania leaders for a place in the finals.