The Kenyan recorded a time of 2:04:44, the second-highest in the event's history, to edge out his compatriot Martin Lel and 2010 winner Tsegaye Kebede in second and third respectively.
"I knew when I went away they have to work very, very hard to beat me as I was feeling very good in myself," he told BBC Sport.
"I am sorry I didn't [break] the record but winning is the most important thing for me. I feel a little tired now, but I am happy and tired."
Lee Merrien was the first Brit to make it past the finishing line, coming in 17th with a time of 2:12:00, marginally failing to make the grade for London 2012.
"I'm pretty gutted. I'm very disappointed," he said.
"After three or four miles we were 100 yards behind the pacemakers and, from six and seven miles, I was forcing the pace at the front of the group and did a lot of the work.
"From halfway I was on my own for the rest of the race and I knew I was still at 2:12 pace but had to pick it up, and to do that on your own and into the wind was tough.
"I was just trying to take the atmosphere in towards the end because this might be the closest I get to the Olympics."
Elsewhere, Mary Keitany took first place in the women's race to cap off the Kenyan dominance of this year's event.