Midfielder Shunsuke Nakamura was among the scorers for the visitors, forced to qualify for the tournament after losing the third-place playoff to South Korea two years ago.
"I'm pleased to finish the year on a winning note," Japan coach Takeshi Okada told reporters. "We should have scored more with the chances we had."
German-based midfielder Makoto Hasebe lashed a fierce right-foot shot into the top corner from 25 metres to put Japan ahead in the 32nd minute.
Japan, who held 2010 World Cup hosts South Africa to a 0-0 draw in Port Elizabeth at the weekend, added a second goal in the 74th through a header from substitute Hisato Sato.
Nakamura, of Spain's Espanyol, curled in a free kick 10 minutes later before striker Shinji Okazaki converted a penalty in the last minute for his 15th goal in 20 internationals.
The "Blue Samurai" have nine points from four matches in Group A, putting the three-times Asian Cup champions within reach of the finals in Qatar.
Hong Kong remain at the foot of Group A without a point and are all but out of the running for a place at the finals.
Hosts Qatar, Asian Cup holders Iraq, 2007 runners-up Saudi Arabia and third-place playoff winners South Korea have already qualified.
India are also assured of their spot courtesy of victory in last year's AFC Challenge Cup.
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