He became the first Ugandan to win the event and he did so on a difficult day for long-distance runners. Of the 105 elite competitors who started the race, 20 did not finish.
Kiprotich did not try to stay with the early pace in the belief that it was too fast for anyone to maintain and that turned out to be the right decision.
The leaders eventually came back to him and when he put on a burst at the 24-mile mark no one could keep up.
Kiprotich completed his run through the streets of central London in 2 hours, 8 minutes, 1 second.
It was the first medal of the Olympics for Uganda, which became the 85th country to win one.
Abel Kirui of Kenya won the silver medal and Wilson Kipsant Kiprotich of Kenya was third -- 70 seconds behind Kirui.
American Mebrahtom Keflezighi, who finished second at the Athlens Olympics eight years ago, wound up fourth. He was followed by Marilson dos Santos of Brazil, Kentaro Nakamoto of Japan and Cuthbert Nyasango of Zimbabwe.
Runners from Ethiopia were exected to challenge, but none of the three competitors from that country made it to the finish line.
The marathon traditionally finishes in the main Olympic stadium, but organizers of these Games chose to send the runners through the heart of the city past some of its most well-known landmarks. The finish came in front of Buckingham Palace.