His lightning fast run of 2hr 02min 57sec was the second year running that the record had been broken in Berlin, the previous best being 26 seconds slower -- the 2:03:23 set over the same course last year by compatriot Wilson Kipsang.
The performance by the 30-year-old, a former farmer from western Kenya's high-altitude Rift Valley region, delivered a new benchmark in human endurance and cemented the Kenyans' total dominance of international road racing.
"As the race went on, I saw I could do it, I'm delighted to have won," the modest Kimetto said after making history and nudging world leading times close to the mythical 2-hour barrier.
Kimetto, the pre-race favourite, was part of a seven-man breakaway group after 20km, which included fellow-Kenyans Emmanuel Mutai and Geoffrey Kamworor.
But Kimetto shook off Mutai four kilometres from home and crossed the line in record time over what is regarded as the world's fastest marathon course. Mutai finished second, also inside the previous record time with a run of 2:03:13 - illustrating the depth of Kenya's talent.
Ethiopia's Abera Kuma a long way back in third in 2:05:56.
Kimetto hails from the town of Eldoret - a part of the country that has produced some of the most dominant distance runners in history and is emerging as the world's training capital.
He was working as a farmer in an impoverished rural area before he took up running in his mid-20's, joining the training group of Geoffrey Mutai - a Boston, Berlin and two-time New York marathon champion and the former holder of the unofficial world best, a 2:03.02 set in Boston.
His first major win came in Nairobi's Half Marathon in 2011, and he went on to finish second behind his training partner Mutai in the Berlin Marathon in 2012.
His 2:04.16 was the fastest marathon debut in history, and notable as he is one of a new breed of Kenyan road racers who do not have a track pedigree.
In 2013 he won the Tokyo Marathon, setting a course record of 2:06.50, and then the 2013 Chicago Marathon in a course record of 2:03.45 - where he also beat Emmanuel Mutai into second place.
In the women's race, Tirfi Tsegaye led an Ethiopia 1-2, winning in 2:20:18 from Feyse Tadese (2:20:27) - failing to break the 2:20 barrier and still a way off the 2:15.25 set by Britain's Paula Radcliffe in London in 2003.
Shalane Flanagan of the United Statges was third in 2:21:14, a personal best but short of the American record.
Around 74,000 people applied to take part in this year's marathon, with the 40,000 places being given away by ballot.
Although fewer fancy dress costumes were on display than other major marathons such as London, there were still some colourful participants.
The most serious incident during the marathon appears to have been suffered by a Berlin politician.
Bernd Krömer, the city's secretary for internal administration, collapsed between the 35km and 40km mark. The 58-year-old was resuscitated by medics and taken to hospital.