30-year-old Kipchoge recorded a winning time of two hours, four minutes, 42 seconds.
Wilson Kipsang followed in five seconds later while world record holder Dennis Kimetto completed a Kenyan sweep of the top three places by finishing third.
Kipsang said: “I’m happy for my friend to have won and for me as defending champion to run a good time and get second place, I’m really happy. It was a very tough race but a fantastic one.”
Tigist Tufa crosses the finish line
In the women’s race, Ethiopia’s Tigist Tufa ended Kenya’s domination of the women’s race at the London Marathon with a shock victory.
Radcliffe, meanwhile, bid an emotional goodbye to competitive marathon running with a time of 2:36.55.
The 41-year-old was cheered across the finish line as she bowed out on a stunning athletics career which saw her break the world record (of two hours 15 minutes 25 seconds) in London in 2003.
Speaking after crossing the finishing line, Radcliffe said: “I didn’t care about the time all the way round and I just wanted to thank as many people as possible.
“I went off way too fast and then it got more and more emotional. It was just amazing the whole way round.”
Paula Radcliffe after the London Marathon
28-year-old Tufa, who was only the ninth-fastest in the field, seized a cagey race by the scruff of the neck in the closing stages to pull clear of the field and was able to wave to the crowds as she came down The Mall to win by 18 seconds from Mary Keitany.
It was the biggest win of her career and ended four years of domination by Kenya’s women in the capital.
She crossed the line in an unofficial time of two hours 23 minutes and 22 seconds to become the first Ethiopian women’s champion since Derartu Tulu in 2001.