Korir, 29, a graduate of the University of Louisville in Kentucky, finished in two hours 12 minutes and 40 seconds, the slowest Boston winning time since 2007 and almost 10 minutes slower than the world's fastest time set last year by countryman Geoffrey Mutai.
Levy Matebo came in second and Bernard Kipyego was third while Mutai, the world's top-ranked marathon runner, dropped out of Monday's race at the 30-kilometer mark due to cramps.
Kenya also notched a sweep in the women's race. Behind Cherop's winning time of two hours 31 minutes and 50 seconds were Jemima Jelagat Sumgong, dropped in a furious last-minute dash by the winner, and Georgina Rono.
"We started slowly, we did not start fast like last year," Cherop, who finished third in 2011, told reporters. "I was really prepared this time around ... it's not my first time running in the heat and humidity."
Defending champion Caroline Kilel dropped off the lead pack in the second half of the race and was seen taking a walking break a few miles from the finish. Shortly before slowing, the slender Kenyan took a slight body check at a water stop.
Temperatures were above 80 Fahrenheit (26.6 Celsius) even as the speediest elite runners made their way toward the end of the 26.2-mile course.
Race organizers had urged many non-elite runners to not start the race due to dangerous conditions, and several thousand took up an offer to defer their entries to 2013.
Altogether, six of the 17 elite women and four of 20 elite men runners did not finish the race. Race organizers ramped up their emergency services in anticipation of a wave of heat-related injuries.
In the men's wheelchair division Canadian Joshua Cassidy set a race record at 1:18:25, two seconds below the previous mark set in 2004 by South African Ernest Van Dyk, nine-time winner.