Compatriot Troy Merritt had raced into the lead with a strong third round but faded on Sunday, mixing four birdies with a bogey.
The Barracuda Championship - at the Montreux Golf and Country Club - uses a Modified Stableford format, which allocates points based on the number of strokes taken at each hole.
Eight points are awarded for an albatross, five for an eagle, two for a birdie, zero for a par, minus one for a bogey and minus three for a double bogey or worse.
Morikawa, 22, followed Saturday’s 13 with a 14 to take the title - his first on the PGA Tour - with 47, three better than Merritt and seven more than John Chin and Robert Streb who tied for third.
Scotland’s Martin Laird finished in a four-way tie for seventh on 37 points, scoring five birdies in the fourth round.