The 25-year-old clocked two hours 06.25 minutes over the 42.195km course to beat Mathew Kisorio by 11 seconds and Ernest Ngeno by 16 seconds.
The women's race started later so that the athletes would arrive at the finish line at roughly the same time as the men. Kenya's Betsy Saina crossed the line shortly after Lonyangata to win in two hours 22.55 minutes.
Kenyan Ruth Chepngetich was second and Ethiopian Gulume Chala took third place.
The women and men climbed on the podium together.
(Reporting by Julien Pretot; Editing by Toby Davis)
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