The second place finisher, two-time victor Lelisa Desisa, finished one second slower, according to race officials.
Ethiopia's Worknesh Degefa won the women's elite race by 42 seconds with a time of 2:23:31, holding off Kenya's Edna Kiplagat (2:24:13), Jordan Hasay of the United States (2:25:20), Meskerem Assefa of Ethiopia (2:25:40) and Des Linden of the US (2:27:00).
Degefa's only other marathon experience might have been on the flat roads of Dubai, but the 28-year-old - whose PB of 2:17:41 from January puts her fourth on the world all-time list - wasn't put off by Boston's hills.
Last year's second-place finisher, full-time nurse Sarah Sellers of Tucson, also improved her time from last year but finished 19th.
Kipkemoi was third in 2:08:07, while Kenya's Felix Kandie was fourth in 2:08:54 and Kirui fifth in 2:08:55.
Woknesh Degefa ran alone for the last 20 miles winning the women's race.