Already a silver medalist and US record-holder in the 10,000 meters, he ran the fastest marathon time ever for an American in the Summer Games: 2 hours, 10 minutes, 5 seconds.
It was the fastest-ever debut by an American woman, Runner's World says.
Policewoman Kiplagat produced a superb performance to win the women's race on her debut in 2:21.52.
Meb Keflezighi, who won the Boston Marathon the year after the bombings, stopped at the finish line Monday for an emotional exchange with Martin Richard's family.
Kiplagat, the 2011 and 2013 IAAF World Champion in the marathon, finished with a time of 2:21:52.
American Jordan Hasay, who is part of Nike Oregon Project, was third, and Desi Linden, in Brooks, was fourth.
This story will be updated. "I said to my coach immediately after the incident, 'I have to finish this race now because if I drop out of this race, nobody's going to believe that women are serious.'" And so she persevered and finished.
Absent Kenyan Eliud Kipchoge won the overall World Marathon Majors title despite not competing in Boston.
As the Olympic bronze medalist, Rupp had to be considered one of the pre-race favorites in a field that wasn't extraordinarily deep by some Boston standards.
Still, Rupp had no answer for marathon rookie Kirui over the final stretch of the course.
"American distance running is looking good today", said sixth-place finisher Abdi Abdirahman, a Somali immigrant and Tucson resident who is a four-time Olympian.
"I wouldn't have been able to do it without you all", Sanchez said.
For Kirui, even when he was running shorter distances, he had his eye on Boston.
It was a Swiss sweep in the wheelchairs, as Manuela Schar won the women's title with a course record of 1:28:17.
No women's World Marathon Majors victor has yet been named pending the outcome of a doping investigations into series leader Jemima Sumgong.
Keflezighi won the men's division of the first marathon after the 2013 bombings, becoming the first American victor since 1983.