Watabu, who needed 20 holes to beat Tim Feenstra in the semifinals, never trailed in the final and led by as many as 7-up.
The 21-year-old Kim, who was a member of the victorious 2005 USA Walker Cup team, rolled into the finals with a 6-and-5 win over Kevin Larsen in the semis.
Watabu, who is a recent graduate of the University of Nevada, opened with a birdie on the first. Kim battled back to even the match with a birdie of his own on the third at Gold Mountain Golf Club. However, that was the only hole Kim would win in the opening 18.
The 22-year-old Watabu regained a 1-up lead thanks to Kim's bogey on the par-3 fifth. The duo halved the next six holes before Watabu extended his lead to 2-up at the 12th.
Kim, who was the medalist at the 2005 Public Links Championship, bogeyed 13 and another bogey at the par-3 16th left him 4-down. Watabu birdied the 18th to head to the afternoon session with a 5-up cushion.
Watabu quickly padded his lead once the afternoon session began. The Hawaiian birdied each of the first two holes to stretch his lead to 7-up through 20 holes.
Kim, a senior-to-be at the University of Oklahoma, poured in three birdies in a four-hole span from the 22nd hole to cut his deficit to 4-down. They halved the next three holes, though.
Watabu birdied the 29th to go back 5-up. Kim, trying to fight off being closed out, birdied the 32nd hole to get back to 4-down with four to go.
The match was over one hole later when the finalists both made pars.