Bekele's winning time of two hours, 3 minutes and 3 seconds was six seconds outside Dennis Kimetto's world record, also set in Berlin in 2014 and is the second best time.
"I wanted to set a personal best and it's a fantastic time, but it's a little disappointing to miss the world record by so little," Bekele said after the race.
Bekele and Kipsang opened a considerable lead over the rest of the field and ran shoulder-to-shoulder until Bekele pulled away with about two kilometers to go.
Evans Chebet of Kenya was third in 2:05:31.
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Bekele is considered one of the greatest distance runners of all time. He won three Olympic titles and five world championship golds and is the world record holder over 5,000 and 10,000 meters.
But he had been slow getting into the marathon, with his previous best of 2:05.04 set in his debut in winning the Paris race in 2014. He was third in London in April, after battling an Achilles' tendon injury.
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