Brigid Kosgei of Kenya was second with Tadelech Bekele of Ethiopia third.
Kipchoge's wife Grace Sugut who attended the session said the celebrated marathoner had assured her that he would win.
Farah certainly lasted the distance all right, only not the pace set by the indomitable Eliud Kipchoge, the Kenyan with the best marathon record in history when it comes to lasting the distance and the pace.
"The crowd really got behind me, it was an awesome atmosphere".
The Kenyan led the way with Ethiopian great Kenenisa Bekele and last year's victor Daniel Wanjiru of Kenya also in the mix.
Farah twice struggled to find his bottle at the feeding stations littered around the course at the 10km and 20km marks, and seemed agitated as he ran over to the motorcycle stewards, anxiously asking whether he could get any water.
Tola Shura Kitata of Ethiopia stayed with Kipchoge until close to the end but the 2015 and 2016 champion strode clear to win with a time of 2:04:17 - two minutes 20 seconds off the world record.
He beat Steve Jones' 33-year-old British record.
The guys went for it, they were on for world record pace, so it was do or die.
"I came to London to run a handsome race and today I ran a really lovely race", said Kipchoge.
"It's so different to the track". It's incredible. It's a different pain, different training but I've really enjoyed it. Some of the staff tried to take a picture rather than give me a drink at the start.
The 35-year-old noticed his drinks bottle had gone missing around the 10-mile (1.6km) mark and had to turn back for it. "I got 5th today & in dire need of a holiday time for some family time".
He told the BBC: "I am knackered. It's so far-reaching. We fully needed it and not just us - for the community and the rest of the London Fire Brigade who attended". This year's was the hottest one ever.
"I'm satisfied with the result".
Race organisers had previously urged runners to reconsider aiming for personal bests and suggested ditching fancy dress costumes.
"My aim is to run another marathon in the autumn and then see what happens in the summer of 2019".
Kenyan Cheruiyot, 34, took advantage of failed attempts by last year's victor Mary Keitany and runner-up Tirunesh Dibaba to break Paula Radcliffe's 15-year-old world record.
Keitany was a colossal 32 seconds ahead of Radcliffe's 10-mile time, with Ethiopian rival Tirunesh Dibaba for company.
Rob Smith took victory in the T51/52 classification, beating Cristian Torres by more than two minutes while Derek Rae stormed to top spot in the T45/46 race in a time of 2:36.13.