Vivian Cheruiyot made it a double for Kenya, setting a new personal best as she won the women's race in 2:18.31.
He crossed the finish line with a time of 2:06.32, beating a British record of 33 years, which was previously set by Steve Jones.
Cheruiyot took advantage of failed attempts to break Paula Radcliffe's 15-year-old world record by last year's victor Mary Keitany and runner-up Tirunesh Dibaba.
Kipchoge, who skipped last year's race to attempt a sub-two-hour marathon in Italy, could not break Dennis Kimmetto's world record as high temperatures made running conditions hard in the English capital.
"I came to London to run a attractive race and today I ran a really lovely race", said Kipchoge. Find us on Facebook too! I went with it and hung in as much as I could. It's incredible. It's different pain, different training but I've really enjoyed it.
"The guys just went for it, at world record pace".
The men's race went out at a blistering pace, and Farah stayed with the group until a freaky incident when he missed his drinks bottle around the 10-mile (16-kilometer) mark, which delayed him after a heated exchange with a steward.
"I was saying to the people on motorbikes to tell the staff to be a bit helpful instead of taking pictures".
Vivian Cheruiyot savours her victory after winning an Olympics gold medal in 5,000m in Rio de Janeiro, Brazil past year. I've got a lot to learn about the marathon but as long as I can keep doing it. But Dibaba was soon reduced to a walking pace to leave Keitany with only her two male pacemakers for company.
Mary Keitany and Tirunesh Dibaba, who were first and second respectively in 2017, threatened to break Paula Radcliffe's world-record time but faded over the second half of the course.
"The reason it was so good for me today was because I started slowly. I want to thank everyone out there for their support".
The thousands of sun-bathed British fans had already found plenty to cheer as David Weir outsprinted Marcel Hug to clinch an eighth wheelchair crown on his 19th appearance at the race, while Madison de Rozario claimed Australia's first women's wheelchair title as she snatched victory from four-time champion Tatyana McFadden.
Second place in each received $30,000, third got $22,500, fourth $15,000.