The former world champion finished in 3:35:59, almost a minute clear of Australia's Jared Tallent, who took silver for the second Games in succession, with China's Si Tianfeng claiming bronze.
Ireland's Robert Heffernan was fourth in a national record of 3:37.54, just holding off Russia's Igor Erokhin on the line as both athletes were given the same time.
Si looked on course for victory when he wiped out a 20-second deficit and went clear of the field at the 35km mark, but when he faded Kirdyapkin took over at the front and was never in danger of being caught.
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