The 33 year-old clocked two hours, one minute and 39 seconds, beating compatriot Dennis Kimetto's mark - also set in Berlin four years ago - by one minute and 18 seconds.
Kenya's Eliud Kipchoge (second right) takes the start among other top runners at the Berlin Marathon on September 16, 2018 in Berlin.
"I lack words to describe this day", said a beaming Kipchoge, a former world champion over 5000m and marathon gold medallist at the Rio de Janeiro Olympics in 2016.
Kenyans from all walks of life suddenly donned their patriotic caps at around midday on Sunday moments after marathoner Eluid Kipchoge shattered the world record in Berlin.
"They say you can miss it twice but not a third time. So I want to thank everyone who has helped me", said Kipchoge, who had won in Berlin in 2016 and 2017.
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His three pacemakers were pushed to the limit to keep the tempo high as Kipchoge dipped well below world-record time by the halfway mark.
Yet even after the last pacemaker peeled off after 25km, Kipchoge showed no sign of slowing as thousands of Berliners egged him on. "@EliudKipchoge is a monster congrats champ I will live to remember this day it will take a generation to see another run like that", former Boston Marathon champion Wesley Korir added on Twitter. It was really hard, but I was truly prepared to run my own race. "That's what pushed me in the last kilometres", Kipchoge said.
Organizers initially put Kipchoge's time at 2 hours, 1 minute and 40 seconds, but later reduced it by one second.
Kipchoge, the Olympic champion, had always been called the greatest marathon runner of all time but, despite winning nine of his past ten marathons, the world record had eluded him until yesterday when he barely saw a rival before winning the Berlin Marathon in 2hr 1min 39sec. Canadian Brent Lakatos won the men's wheelchair race for his first marathon victory.
A proud Kenyan President Uhuru Kenyatta congratulated Kipchoge, and his fellow countrymen - second-placed Amos Kipruto and third-placed Wilson Kipsang - as the East African trio made a podium sweep.