In a stunning upset Kipchoge, who had won all of his previous four London Marathons and had not lost over the distance in seven years, dropped alarmingly off the pace around the 22-mile mark.
Kipchoge, the 35-year-old world record holder, had no answer as a seven-strong lead group edged away from him, and he ended up finishing down in eighth.
Sir Mo Farah, who was part of the race as a pacemaker, admitted he was astounded by Kipchoge's defeat.
"It was a shock for all of us. We had expected him to win by miles, considering what times he has run," Farah told the BBC.
"But that happens, it's sport. It was a good field. It's part of racing, it's part of sport, it happens."
Instead the title was up for grabs and it was Ethiopian Kitata who snatched it in two hours, five minutes and 41 seconds, pipping Kenya's Vincent Kipchumba on the line after a thrilling sprint finish.
A faster race was predicted due to the nature of the course - 19.7 laps of St James's Park rather than the traditional street route - but the incessant rain and autumnal temperatures put paid to that.
With Kipchoge's great rival Kenenisa Bekele, the second fastest marathon runner in history, missing through injury the stage looked set for a fifth victory for the Kenyan superstar.
But despite the slow pace he came up short and Kitata took full advantage, as Kipchoge was beaten for the first time since he came second in Berlin in 2013.
Kipchoge revealed afterwards that he had a problem with his right ear which hampered his race and ultimately cost him the chance of another win.
"I'm very disappointed but, all in all, this is sport," he said. "I got a blocked ear the over last 15km. I tried to keep going and make sure I finished, to show there is always hope in the world. It's not the end of the world that I can't win.
"It's not suicide. This is sport and we need to embrace ourselves. I want to congratulate the top finishers for bringing hope to the streets of London at this time of Covid-19."
This year's competitors pounded just four streets of London rather than the traditional route from Blackheath to Buckingham Palace, with no crowds and no fun runners due to the coronavirus pandemic.
The home straight remained the same, down The Mall, and it staged a nailbiter as Kitata got the better of Kipchumba by a second.
Kitata revealed he had taken the advice of Bekele, who was runner-up last year.
He said: "I prepared very well for this race, kept my concentration. Kenenisa trained me and advised how I should run this race. I trained for the same course. I am very happy to win the race."
Jonny Mellor was the first British man across the line in a time of 2:10:38, and compatriot Ben Connor also finished inside the Olympic qualifying time.
In the women's race Brigid Kosgei defended her title, the 26-year-old world record holder comfortably winning her duel with fellow Kenyan Ruth Chepngetich.
Kosgei broke for home with seven miles to go leaving Chepngetich, who had looked the stronger in the mid-stages of the race, far behind.
"The weather was not good so we struggled," said Kosgei. "I struggled up to the moment I finished.
"We have not prepared well due to the pandemic. I will be prepared for good results next year."
Chepngetich, the world champion, eventually lost second place to fast-finishing American Sarah Hall.
There was disappointment for the two big British hopefuls, Lily Partridge and Steph Twell, who both pulled out well before the finish.
The British title instead went to Natasha Cockram, who finished outside the Olympic qualifying mark in 2:33.19, four seconds ahead of Naomi Mitchell.
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