Donald fired a closing 68 to finish the week 16 under par, with Japan's Hideki Matsuyama second after a 67 and compatriot Koumei Oda's 64 lifting him to third spot.
Four clear with a round to go, Donald's first win since the BMW PGA Championship at Wentworth Club in May never looked in doubt after he birdied the fourth, eagled the seventh and birdied the next.
He did bogey the next two, but then came seven pars and a birdie on the long 18th.
Afterwards Donald told his twitter followers: “Loved my week here in Japan - the Dunlop Phoenix is a great event, on a great course, great food, great beer....it's just great!”
