After a scoreless first half, the hosts got off to a flying start in the second when Shunsuke Nakamura opening the scoring in the 47th minute. Forward Keiji Tamada was brought down just outside the Bahrain area, and the Celtic playmaker curled the ball into the net via a deflection off Abdulla Marzooq.
Earlier, with three forwards, the Japanese played aggressive from the beginning but found it difficult to break the last line of defence. Their best chance in the first half came in the 25th minute, when captain Yuji Nakazawa jumped for a header off Endo's corner, only to see defender Mohamed Hubail clear.
After taking the lead, defender Atsuto Uchida was free in front of the Bahrain goalmouth, but failed to hit a shot in the 54th minute, while forward Tatsuya Tanaka's effort was saved by Jaafar four minutes later. In the 64th minute, Japan countered well but Uchida's shot hit the crossbar.
Japan now have 11 points from five matches, and lead the five-team pool. Australia have ten points but have a game in hand. Bahrain have just four points from five contests.
The top two teams in the group will qualify for South Africa 2010, while the third-placed team will have to survive play-offs.