In wet and windy conditions, 2022 champion Chebet, from Kenya, took his time before surging away in the closing stages to become the first man to defend the Boston crown since compatriot Robert Kipkoech Cheruiyot completed a hat-trick of victories between 2006-2008.
Chebet finished in a time of 2hr 5min 54sec, with Tanzanian Gabriel Geay finishing second in 2:06:04, and Kenyan Benson Kipruto third in 2:06:04.
Another Kenyan, Hellen Obiri, stormed to a brilliant victory in the Boston women's race on Monday, winning a thrilling closing duel with Amane Beriso to take the title in only her second race over the distance.
Obiri, a two-time world champion over 5,000m, surged home in 2hr 21min 38sec to see off the challenge of Ethiopia's Beriso over the final mile.
Beriso took second in 2:21:50 while Israel's Lonah Salpeter took third in 2:21:57.
Two-time Olympic champion and world record holder Kipchoge - who had been bidding to add the Boston crown to previous marathon victories in Berlin, Tokyo, London and Chicago - trailed home in sixth place in 2:09:23, around three-and-a-half minutes adrift of Chebet.
Kipchoge had looked in prime form over the opening stages, coolly leading a group of 10 runners through the halfway stage in 1:02:19.
The Kenyan icon still looked in control when the leading group started to thin after around 16 miles, with the pace picking up as the undulating Boston course made its descent.
But the complexion of the race changed in mile 19 when Geay made what turned out to be a huge move that broke Kipchoge's resistance.
As the pack gave chase to Geay, the world record-holder was rapidly left behind and was soon nearly 100 meters off the pace.
Geay remained in the lead through 24 miles in a leading trio alongside Chebet and Kipruto.
But Chebet and Kipruto kicked on in the final two miles and Chebet led with a mile to go before pulling away to retain his crown.
Geay staged a late rally to take second from Kipruto.