Hamilton, the leading money winner on the Japanese tour this season, carded seven birdies at the Nidom Classic course for a 5-and-4 victory over Miyamoto.
Elsewhere, New Zealand's David Smail birdied the final hole for a 2-up victory over Tsukasa Watanabe, while last year's leading money winner Toru Taniguchi was a 3-and-1 winner over Kim Jong-duk of South Korea.
South Korea's S.K. Ho knocked down six birdies on his way to a 2-and-1 win over Shinichi Yokota.
The Japan PGA Matchplay Championship features a field selected on the basis of money rankings.
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