"My only words are: 'Thank you!'," said Kipchoge, who sprinted into the lead after 100 metres and never relinquished his supremacy.
"I was prepared to run my own race early so I wasn't surprised to be alone,” he added. “I have trained so well for this race and I am just so incredibly happy to have finally run the world record as I never stopped having belief in myself."
Acclaimed as the greatest marathon runner of the modern era, Kipchoge has dominated the course since making his debut in Hamburg in 2013 after a successful track career in which he won world championship gold and silver medals in in the 5000m and Olympic silver and bronze over the same distance.
He has notched up 10 wins from the 11 marathons he has raced including gold over the distance at the Rio Olympics in 2016.
In Berlin on Sunday, Kipchoge passed the five kilometres mark in 14 minutes and 24 seconds.
But shortly after 15 kilometres, which was reached in 43 minutes and 38 seconds, two of the three pacemakers were unable to continue and withdrew from the race.
The final pacemaker, Josphat Boit, led Kipchoge through the half-way point before dropping out at 25 kilometres, which had been covered in 1 hour, 12 minutes and 24 seconds.
Running alone with 17 kilometres left, Kipchoge maintained his form well into the closing stages to smash Kimetto's mark. "Yes, it was tough running alone,” admitted Kipchoge. “But I was confident. I had said that I would be running my own race and following my planning.”
Fellow Kenyans Amos Kipruto and Wilson Kipsang finished second and third while their compatriot Gladys Cherono claimed the women’s race in 2 hours, 18 minutes and 11 seconds, a course record and world leading time.
The Ethiopians Ruti Aga and Tirunesh Dibaba came in second and third.