Pacemakers lead out the field past the Tokyo Government Building after the start of the Tokyo marathon (AFP)
Kipchoge pulled away from countryman Amos Kipruto at around the 35km mark but was unable to beat the 2:01.39 he clocked at the 2018 Berlin marathon.
The 37-year-old was not helped by a wrong turn by the leading pack after about 10 kilometres, which cost the runners around 10 seconds and upset their rhythm as they doubled back on themselves.
Kipchoge joined a select club of athletes last year when he defended his 2016 Rio Olympics marathon title at the pandemic-delayed Tokyo Games in Sapporo.
"I'm really happy. I'm excited again to be in Japan, especially after winning the Olympic Games last year in Sapporo," he said.
"I really, really, really appreciate the crowd. I think the Japanese are really helpful. That's why I say in the press that I run strong in Japan."
Kipruto finished second in 2:03.13.
Kenya's Brigid Kosgei, another world record holder, won the women's race in 2:16.02.
Kipchoge was making his Tokyo debut in one the six major marathons alongside New York, Berlin, Chicago, London and Boston.
He has already won in London, Chicago and Berlin and it is one of his career objectives to land all six.
Kipchoge said in January that he would be seeking to make it a record-breaking three consecutive Olympic titles at Paris 2024.
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