The in-form 30-year-old, a winner in London in April, proved a master of the flat, inner-city course, regarded as the fastest in the world, even as his insoles slipped out of his shoes early in the race, winning ahead of fellow Kenyan Eliud Kiptanui and Ethiopia's Feyisa Lilesa.
"At some point they started coming out but I had no time to remove them," Kipchoge told reporters. "But when you run without soles there is a lot of impact. There was a lot of pain with every step."
"The world record was really my aim but it was not my day for it," he said. "But I ran a personal best and I am happy and I will come back next year for it."
Fellow Kenyan Gladys Cherono clocked 2:19:25, winning the women's race ahead of Ethiopians Aberu Kebede and Meseret Hailu.
Kipchoge, a former double Olympic medallist at 5,000m, quickly led a group of six runners, including fellow Kenyans Emmanuel Mutai and Geoffrey Mutai, as they quickly broke away from the pack on a sun-drenched autumn morning.
The Kenyan looked unaffected when the insoles of his shoes started slipping up to his ankles and flapped against his thighs with every step.
But it was Geoffrey Mutai, who won here in 2012 and was one of the pre-race favourites, who dropped back first, failing to keep up with gruelling pace.
Kipchoge, undeterred by his footwear mishap, pulled away after 32 kilometres, gradually building up a 30-metre lead over his rivals and extending it as he cruised to victory with his new-found footwear wings still flapping.
(Reporting by Karolos Grohmann; editing by Sudipto Ganguly)
