Kipruto ran flat out through the final 50 metres to hold off a late fight from Alexander Mutiso, breaking the tape by a fraction of a second in a photo finish, with the 2021 winner Albert Korir finishing third (2:08:57).
The Paris bronze medallist Obiri, who won in 2023, was running shoulder to shoulder with runner-up Sharon Lokedi (2:20:07) before pulling away ahead of the final turn to break Margaret Okayo's 22-year-old course record of 2:22:31.
Last year's winner Sheila Chepkirui (2:20:24) was third.
The five-borough classic capped the World Marathon Majors calendar for the year.