American CJ Albertson set an aggressive early pace to lead the men's field by two minutes and 13 seconds through the first half but saw his headstart disintegrate over hilly terrain after the 20-mile mark, as a tight pack overtook him.
Kipruto, who won the Prague Marathon in May, pulled away with less than 10 kilometres to go and had secured a commanding 41-second lead heading into the last mile, absorbing the cheers along Boylston Street as he broke the tape in two hours, nine minutes and 51 seconds.
Ethiopians Lemi Berhanu and Jemal Yimer finished second and third, respectively.
In the women's race, a crowded pack stuck together through the first 25 kilometres before Kipyogei, who won the Istanbul Marathon in 2020, made her move, securing a 10-second lead over the rest of the field by the 30-kilometre mark.
Ethiopia's Netsanet Gudeta quickly challenged her but Kipyogei proved too powerful, again pulling away to win the race in two hours, 24 minutes and 45 seconds.
Edna Kiplagat, who won in 2017, and Mary Ngugi finished second and third, respectively, to complete a podium sweep for Kenya.