"It wasn't the plan because I thought I would go with my first pacemaker through 30 kilometers", Kipchoge said.
It was a clean sweep for Kenya after Amos Kipruto came in second with 2:06:23 while Wilson Kipsang won with 2:06:48 as the unofficial time.
Kipchoge came agonizingly close to sporting immortality by almost running the first sub two-hour marathon a year ago.
Manuela Schar also set a world record while winning the women's wheelchair race in 1:36:53.
Kipchoge, 33, is the reigning Olympic champion in the marathon and has run the fastest recorded time over 26.2 miles-a blistering 2 hours and 25 seconds- as part of a Nike-sponsored marketing event previous year that wasn't a ratified race.
He won the London Marathon for a third time earlier this year and is the Olympic champion over the distance.
Cherono won in 2:18:11, breaking the previous course record (2:19:12, Mizuki Noguchi, 2005) by over a minute. With already half a marathon behind him, the Kenyan nevertheless managed to run an incredibly quick time.
Kipruto and Kipsang's times are an indication of how Kipchoge's pace blew the race apart from the outset.
Boosted after leaving Boit, he surged, running the 27th kilometre in just 2:51 - seven seconds faster than necessary. "So I want to thank everyone who has helped me", Kipchoge, who previous year took part in the Nike Breaking Two project, where he ran two hours and 25 seconds with the aid of "illegal" in and out pacemakers.
He kept injecting the pace and by the 30km mark, he was a massive 52 seconds inside World Record pace having covered the distance in a time of 1:26:45.
Dubbed the greatest marathon runner of the modern era, Kipchoge produced a fantastic race in the German capital to finally eclipse the one major running accomplishment that had eluded him in his illustrious career.
Kipchoge now adds the official world record to his extensive list of achievements.
Kenya's Eliud Kipchoge crosses the finish line to win the Berlin Marathon setting a new world record on September 16, 2018 in Berlin.
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