Kipchoge ran the final seven kilometers on his own through the streets of Rotterdam to finish in exactly 2 hours, five minutes. Fellow Kenyan Bernard Koech was second in 2:06.07.
Organizers had hoped to break the course record of 2:04.27 set in 2009 by the Kenyans Duncan Kibet and James Kwambai, but pacemakers dropped out regularly as wind hindered the runners.
“I’m happy to win the race,” Kipchoge said. “Next time, I will come for the course record.”
Meanwhile, Getu Feleke of Ethiopia overcame stomach problems in the closing kilometers of the Vienna City Marathon to win the event in a course-record time on Sunday.
Feleke accelerated and left behind a leading group after 30 kilometres.
He finished in 2 hours, 5 minutes, 41 seconds and beat the best mark, set by Henry Sugut of Kenya two years ago, by 1:17.
“In the last two kilometres I had problems with my stomach.
“I could have been faster,” said Feleke, who earned his second career marathon victory after winning in Amsterdam in 2010. Feleke became the first non-Kenyan winner of the Vienna event since 2007.
Alfred Kering finished second in 2:08:28 and fellow Kenyan Philip Sanga came another 30 seconds behind in third.
In cloudy conditions and with temperatures up to 12 degrees, three-time winner Sugut lost touch with the leading group after 20 kilometers and quit the race shortly afterward.
2011 champion John Kiprotich, the only other former winner in the field, couldn’t keep up with the leading pace from the ninth kilometer.
“It was a very good race except for the wind,” Feleke said.
“There was strong wind between the 24th and 26th kilometre and when I was running alone after 30 kilometres.”
Feleke, who set his personal best of 2:04:50 in Rotterdam three years ago, made his debut on the marathon distance in Vienna five years ago.
“This is my lucky city,” Feleke said. “It’s not my best time but it is a great win.”
Anna Hahner of Germany won the women’s race after overtaking leader Caroline Chepkwony of Kenya 300m before the finish.
Hahner came 1:04 short of her personal best as she timed 2:28:59 and beat Chepkwony by 20 seconds. Marta Lema of Ethiopia was third in 2:31:10.
“I just can’t believe it,” Hahner said.
“I was running in fourth and started thinking that reaching the podium could be possible.
“When I was in second, people along the road shouted that Caroline had almost come to a standstill.
“I passed her and just didn’t look back.”
Hahner became the first European winner of the event since Andrea Mayr of Austria five years ago.