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 past year that wasn't a ratified race.
It was the largest single improvement on the marathon world record since Derek Clayton improved the mark by 2:23 in 1967.
"I lack words to describe this day", said a beaming Kipchoge.
A few minutes later Gladys Cherono won the women's race in Berlin in a course record of 2:18:11, making her the fourth fastest woman in history behind Paula Radcliffe, Mary Keitany and Tirunesh Dibaba.
The Kenyan defended his 2017 title in the German capital, pulling ahead of other runners early on amid flawless conditions. But shortly after 15 kilometres, which he reached in 43:38, two of the three pacemakers were unable to continue and withdrew from the race.
Running alone with 17 kilometers left, Kipchoge then sped up.
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Top put Kipchoge's new time into context, the last time the marathon world record was beaten by over 30 seconds was when Paul Tergat lowered Khalid Khannouchi's mark to 2:04:26.
With good weather on the right course, there was little doubt after Monza that Kipchoge would soon seal his legacy by owning the world record.
Ahead of the race, Kipchoge was more reserved about his expectations and told reporters that he was simply aiming to lower his personal best of 2:03:05.
"It wasn't a plan (running without pacemakers) because I thought I would go with them to 30km but it was unfortunate".
"I'd said I was running my own course following my planning and I was confident".
The marathon organizers dubbed Kipchoge as the greatest marathoner of all times. Kipchoge crushed the majority of the second half by himself- the final pacer dropped out just past 25k- after hitting the half marathon in 61:06.
Race organisers initially timed Kipchoge a second slower, but later corrected the time.