Kiprotich was the surprise winner at last year's London Games but started as one of the favourites in Moscow and became the first non-Kenyan to win the title since 2005.
Ethiopia's Boston marathon winner Lelisa Desisa was second 21 seconds behind in 2:10:12 and compatriot Tadese Tola took third a further 11 seconds back.
Part of a large leading pack for most of the race, Kiprotich began pushing the pace just after the 30-km mark and the group slowly started to break up.
With just over two km to go, the gold was between Kiprotich and Desisa and the Ugandan finally broke his rival as they ran through the Olympic Park to enter the stadium alone, smiling and waving to the crowd.
Peter Some in ninth was the first Kenyan finisher for a team that was missing twice world champion Abel Kirui through injury.
Photograph: Christian Petersen/Getty Images
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