The 34-year-old was looking to better compatriot Dennis Kimetto's mark of 2:02.57 and wrest back the world record he lost in 2014 but was unable to take sufficient advantage of a new course design.
"Today I was really feeling good and the course was very nice," Kipsang said after receiving the trophy.
"I really enjoyed it and I was going for a world record but I think it was a little bit windy and that's why I couldn't run that time."
All six of the world record times recognised by the IAAF have been set at the Berlin marathon, including Kipsang's at the 2013 version.
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Kipsang had said he would be aiming for a mark of 2:02.50 and, running at the front of the field behind a phalanx of blue-shirted East African pacemakers, was on course for it at the 10, 15 kilometre and halfway marks.
At the 30 kilometre mark, only compatriot Dickson Chumba was still with him and 10 kilometres later, he was on his own but slightly off the world record pace.
Gideon Kipketer (2:05.51) passed Chumba (2:06.25) on the final few kilometres to finish second in a Kenyan podium sweep.
The previous best time in Japan was Tsegaye Kebede's 2:05.18 at Fukuoka in 2009, while Mizuki Noguchi's Osaka mark of 2:21.18 had stood for the women since 2003.
Sarah Chepchirchir ended that reign as Kenya also took the spoils in the women's race in 2:19.47, the 32-year-old leading home Ethiopians Birhane Dibaba (2:21.19) and Amane Gobena (2:23.09).
(Reporting by Nick Mulvenney in Sydney; Editing by John O'Brien)
