The Japanese Football Association announced coach Javier Aguirre opted not to include Uchida as the 26-year-old bids to be fit for the second half of the Bundesliga season having been hampered by a long-standing knee injury throughout 2014.
Uchida - capped 72 times by the reigning Asian Cup champions - suffered a tendon injury in his right knee in February before inflammation issues disrupted his pre-season after the World Cup in July.
Naomichi Ueda of Kashima Antlers will replace Uchida at the 16th Asian Cup, which takes place in Australia starting on January 9.
Japan will face Palestine, Iraq and Jordan in Group D.
The Asian powerhouse's first match is against Palestine at Newcastle Stadium on January 12.
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