The 37-year-old running legend broke away from his compatriot Amos Kipruto after about 35 km of running but failed to beat his record of 2:01:39 set in Berlin in 2018. He is also the holder of a an unofficial record, below the mythical 2 hour mark, in 1h59:41, obtained in Vienna in 2019 during an event set up for him.
"I'm really happy. I'm very excited to be in Japan again, especially after winning the Olympic title last year in Sapporo" at the Tokyo Olympics, he said.
He was then defending his title of Olympic marathon champion won in 2016 in Rio de Janeiro.
However, Kipchoge was not helped when, at km 10, the leading group made a mistake in a corner.
He then lost about ten seconds, and his rhythm, when this group came back towards him to resume the correct route.
Kipruto finished second in 2:03:13.
Tokyo is one of the six "major" marathons, along with New York, Berlin, Chicago, London and Boston.
Kipchoge has announced that he wants to win all six of them in his career (before Tokyo, he has already won London, Chicago and Berlin).
He also hopes to triple his Olympic title at the Paris Games in 2024, a record still unmatched.
On the women's side, fellow world record holder Brigid Kosgei, 28, won the race in 2:16:02.
She finished second at the Tokyo Olympics behind her compatriot Perez Jepchirchir.
© 2022 AFP