Chebet picked up his first major victory in two hours six minutes and 51 seconds, with compatriots Lawrence Cherono and Benson Kipruto second and third.
World record holder Kipchoge was among the biggest attractions at the World Marathon Major but lost his momentum around the halfway mark and finished sixth.
Beatrice Chebet added the World 10,000 metres crown to her Olympic gold and World record over the distance, winning the event in 30:37.61 seconds at the World Athletics Championships in Tokyo on Saturday.
Dutchman Abdi Nageeye survived a tense battle through the final mile to win the New York City Marathon in two hours seven minutes and 39 seconds on Sunday
Glimpses from the New York and Beijing Marathons.
