Kenya's Kipchoge had targeted compatriot Dennis Kimetto's world record of 2:02:57 set in Germany's capital last year, which in turn had bettered Wilson Kipsang's previous record of 2:03:23 from 2013.
It was not to be for Kipchoge, this year's London marathon winner, who was hampered by a problem with his shoes early on, but still went on to run the world's fastest marathon time this year and a personal best.
“At some point, the sole came out of my shoe, but I had no time to sort it out and it made things hard as it gave me some pain,” explained Kipchoge.
“It wasn't pleasant on impact with the ground during the race.
“I am happy to have run my personal best, but I had wanted to run the world record.
“I will come back to try again next year.”
Kenya's Eliud Kiptanui was second at one minute, 21 seconds back and Ethiopia's Feyisa Lilesa took third at 2:56.
Having finished second in Berlin in 2013 behind Kipsang, the 30-year-old Kipchoge has now added Berlin to his marathon victories in Hamburg, Rotterdam, Chicago and London.
The lead group passed through the halfway point at 61:53 minutes — down on the world-record pace of 61:30 they had hoped for.
Kipchoge took charge at the 32 kilometre stage, leaving training partner Emmanuel Mutai, who finished second here in 2014, and Lilesa trailing 30 metres behind him.
The winner passed under Berlin's iconic Brandenburg Gate in Kimetto's winning time from last year, several hundred metres short of the finish line.