The Kenyan won in a time of two hours, eight minutes, 44 seconds to beat Ethiopia's Feyisa Lilesa.
MEN'S MARATHON RESULTS
1. Eliud Kipchoge (Kenya) - Gold
2. Feyisa Lilesa (Ethiopia) - Silver
3. Galen Rupp (USA) - Bronze
8. Solomon Mutai (Uganda)
14. Stephen Kiprotich (Uganda)
80. Jackson Kiprop (Uganda)
Uganda ended its 2016 Olympics campaign without getting any medal after falling short in the men's marathon, which featured its final representatives in Rio: defending champion Stephen Kiprotich, Solomon Mutai and Jackson Kiprop.
Red-hot favourite Kenyan Eliud Kipchoge stormed to a runaway gold medal in Sunday's wet men's marathon on the final day of competition at the Rio Olympics.
The Kenyan broke away from his rivals at the 35km mark and romped home to win in a time of two hours, eight minutes, 44 seconds, more than a minute quicker than Ethiopia's Feyisa Lilesa, who took silver.
American Galen Rupp took bronze a further 11 seconds back.
In the shadow of the iconic Christ the Redeemer statue, poking through the rain clouds from high above the city, Kipchoge produced a virtuoso performance as he added gold to the 5,000m silver he won in Beijing in 2008 and his bronze from Athens 2004.
It was a seventh victory in eight marathons for the 31-year-old phenomenon, who won the London Marathon for the second year running in April, coming within eight seconds of Dennis Kimetto's world record of 2:02:57.
A morning downpour put paid to any thoughts of a world record as 155 runners representing 80 countries splashed around the course snaking through the heart of Rio's historic centre in conditions miles removed from the holiday brochures of sun-kissed Rio.
Tokyo champion Lilesa looked in the mood to push Kipchoge while Rupp kept pace after the trio dropped Ethiopian Lemi Berhanu just after the halfway point.
But Kipchoge proved too strong, coming home to loud roars along the home straight of the Sambadrome, home of Rio's famed carnival, before dropping to his knees and crossing himself in celebration.
Paraguay's Derlys Ayala (left) and Argentina's Federico Bruno were burned out upon crossing the finish line
Iran's Mohammad Jaafar Moradi was clesrly in pain near the finish line
Yet USA's Mebrahtom Keflezighi showed he still had some energy left in his tank to do push-ups on the finish line