The 24-year-old was part of a small leading group for the first 30 kilometres before pulling away easily from runnerup Kenyan Bedan Karoki (2:06:48) and strolling to victory.
Karoki's compatriot Dickson Chumba, twice a winner in Tokyo, was third.
With rain lashing down for much of a frigid morning, it was never likely to be a fast race.
Japan fancied their chances of a homegrown male victory for the first time since 2010 but Suguru Osako, who set a new Japanese national record in October, struggled to stay with the leading group and pulled out with an injury 30 kilometres in.
The 27-year-old, touted as Japan’s best hope of delivering Olympic marathon gold when Tokyo hosts the Games in 2020, was distraught as he limped from the route.
Ethiopian Ruti Aga won the women’s race in a time of 2:20:40, edging out compatriot Helen Tola by 21 seconds.
Ethiopians have now won the women’s marathon in Tokyo in six of the last eight editions.
(Reporting by Jack Tarrant; Editing by Ian Ransom)
