The 24-year-old, who had tumbled down the world rankings, showed his quality with a superb final round of 64 to finish on 17 under par at North Berwick.
Australia's Min Woo Lee was the runner-up as local hero Robert MacIntyre faltered in pursuit of a second Scottish Open title, ending four shots adrift alongside England's Matt Fitzpatrick.
MacIntyre, Lee and Fitzpatrick had shared the lead after the fog-disrupted third round was completed earlier on Sunday.
But it was Kim, the only player to avoid a bogey in the fourth round, who pounced from one shot back.
As well as a winner's prize of £1.2 million, Kim's victory also secured his place at next year's US Masters.
"I can't really wrap my mind over it," said an emotional Kim. "It's really special and I'm just at a loss for words.
"Obviously I've had a tough couple years. I got to taste a lot of that humble pie and I got to really learn about myself and I'm still trying to grow, still trying to learn.
"Still got a long way to go. But this one I wanted to dedicate to the people that were in my corner the whole time and struggled with me and who celebrated with me."
Rory McIlroy's third-round 73 left the world number two with too large a deficit to make up, even though he equalled Kim's closing six-under 64, the lowest score of the day.
The Northern Irishman defended his US Masters title in April.
And his performances over the past few days on a links or coastal course in Scotland should encourage McIlroy ahead of the similar conditions he can expect to encounter during next week's British Open at Royal Birkdale, near Liverpool.