The world record holder clocked 2hr 08min 38sec to win gold, becoming only the third man to win consecutive marathon titles.
Abdi Nageeye of the Netherlands claimed silver in 2:09.58, just ahead of Belgium's Bashir Abdi in bronze.
Kipchoge's winning margin of 1:20 was the biggest since Frank Shorter's win in the 1972 Munich Games.
The 36-year-old's victory, his 13th win in the 15 marathons he has raced since 2013, came a day after teammate Peres Jepchirchir secured back-to-back women's Olympic marathon titles for Kenya.
Unlike in Tokyo, where stringent Covid-19 restrictions have forced the Games to be held behind closed doors, thousands of spectators lined the streets of Sapporo, the host city of the 1972 Winter Olympics that lies more than 800 kilometres (500 miles) north of the capital.
The organisers' decision to move the race to the city, however, has backfired, with unseasonally hot and humid temperatures there making for gruelling conditions for the runners.
Sunday's race saw 106 runners representing 45 countries and the Olympic Refugee Team set off from the Odori Park in the heart of Sapporo in temperatures of around 27 degrees Celsius (81 degrees Fahrenheit) and a stamina-sapping 80 percent humidity.
A large lead group of about 50 runners, including Kipchoge, defending world champion Lelisa Desisa of Ethiopia and Rio bronze medallist Galen Rupp of the United States went through 10km in 30:53.
Kipchoge had teammates Lawrence Cherono and Amos Kipruto beside him as running partners.
Two early casualties of note were Uganda's Stephen Kiprotich, who was gold medallist at the 2012 London Games, and a world champion in Moscow a year later, and Ethiopian Shura Kitata Tola, winner of last year's London Marathon in which Kipchoge finished eighth in just his second blip in his marathon-racing career.
Daniel do Nascimento of Brazil, a 2:10 marathon runner, also dropped out with cramp, as Kipchoge led an 11-strong group through the 1:30 mark.
The Kenyan then kicked away on a solo breakaway as the pack split further, opening up a 27-second lead through 35 kilometres (1:46.59).
Cherono, Ayad Lamdassem of Spain, Abdi and fellow Somali-born Nageeye were left battling among themselves in the chasing pack.