The 29-year-old finished in a time of two hours, six minutes and 50 seconds to smash Swiss Viktor Rothlin's 2008 record by 33 seconds but still outside his target of 2:04.
Last year's winner Michael Kipyego finished eight seconds behind Kimetto in the runners-up spot with Bernard Kipyego completing the Kenyan clean sweep of the podium.
It was the first time the Tokyo race had featured as a World Marathon Major with Kimetto's victory putting him top of the standings in the six legged contest that takes place over two years with events in Boston, London, Berlin, Chicago and New York.
Home runners Kazuhiro Maeda (fourth) and Takayuki Matsumiya (ninth) prevented a Kenya-Ethiopia domination of the top 10.
In the women's race, Ethiopian Aberu Kebede followed up her Berlin marathon success by taking the title with a time of 2:25:34.
Her compatriot Yeshi Esayias finished second almost 30 seconds back with 40-year-old Irina Mikitenko of Germany, the World Marathon Majors champion in 2008 and 2009, taking third.
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