The three made a fast start behind Kenyan pacemakers Philemon Rono, Philemon Yator and Edwin Kiptoo, a training partner of Wilson Kipsang. They reached the 5km mark in 14:33 and 10km in 29:16. Kipsang waited until the 35km mark to make his break, with Kipchoge fighting back briefly before the eventual winner pulled away again.
Pre-race favorite Florence Kiplagat of Kenya won the women's race in 2:21:13, a minute and a half slower than her personal best, with compatriot Sharon Cherop second in 2:22:28.
Germany's Irina Mikitenko finished third and set a new over-40 world-best of 2:24:54, almost a minute quicker than the previous mark.
"I'm already 41 but that doesn't mean anything," said Mikitenko. "I feel like I'm 20 with 20 years' experience."
Conditions were cool, but dry and sunny, with only a light breeze.
The race was started by four-time winner Haile Gebrselassie of Ethiopia, who twice set the world record in Berlin.
All eight runners who previously set world records in Berlin were on hand to wave 41,120 runners from 119 nations off at the start.
A 71-year-old man died after collapsing during the inline skating competition on Saturday.
For the first time, a fence was erected around the Tiergarten city park amid increased security in the wake of the Boston Marathon bombing in April, when three people died and about 260 were injured.