The first game between the two sides in qualifying had ended in a 6-0 victory for Takeshi Okada's charges but the hosts made a spirited start to this encounter at the Hong Kong Stadium. However, they first saw their defence breached just after the half-hour mark when Makoto Hasebe drilled home from 25 yards.
Japan rarely stepped out of second gear after that as they patiently built up attacks and did not add to the scoreline until the 74th minute when substitute Hisato Sato headed home. But the visitors' superior stamina clearly showed and they scored a third when Espanyol midfielder Nakamura curled a free-kick into the back of the net before completing the scoring when Shinji Okazaki converted an injury-time penalty.
The victory means Japan remain top of Group A with two games remaining. "We did a very good job," said Okada. "Hong Kong played well and fought hard and attacked on occasion. We were about 70-80 per cent of our total ability today, it was a good performance."
Meanwhile, Bahrain also secured a 4-0 win over Yemen to move level on points with Japan. Ismail Abdullatif opened the scoring in the 20th minute before Baba Fatadi added a second eight minutes later. Hussain Salman then made it 3-0 just after the hour mark before Abdullatif wrapped up the emphatic win with his side's fourth with nine minutes remaining.