Ethiopia’s Mosinet Geremew came in second as his compatriots Mule Wasihun and Tola Kitata came in third and fourth respectively.
“I’m happy to win on the streets of London for the fourth time and to make history,” Kipchoge told BBC Sport.
“The crowd in London is wonderful and that spirit pushed me. From the first kilometre to the last, everybody is shouting. I’m happy to cross the line.”
President Uhuru Kenyatta led leaders including Deputy President William Ruto and ODM leader Raila Odinga in congratulating Kipchoge on his stellar performance.
“Congratulations to #TeamKenya for the excellent performance at the #LondonMarathon. Well done Eliud Kipchoge, Brigid Kosgei and Vivian Cheruiyot for a great finish in your respective races, we are so proud of you for flying the Kenyan flag high,” Uhuru said.