Kim needed 19 holes to beat Matt Harmon in his quarterfinal match, then rolled to a 6-and-5 win over Kevin Larsen in the semifinals.
Watabu defeated Daniel Im 3 and 1 in the quarters, before he outlasted Tim Feenstra 1-up in 20 holes in the semifinals.
Larsen took the first hole against Kim with a par. However, that was the last hole he would win. Kim birdied the second at Gold Mountain Golf Club to even the match.
The 21-year-old Kim birdied five and six, while Larsen bogeyed seven, eight and nine as he dropped five straight holes. He also bogeyed the 10th, but Kim did as well. Kim birdied the 12th to go 6-up and the match was over one hole later as they both parred No. 13.
'For some reason, I just felt more comfortable out there in the afternoon than I did in the morning,' said Kim, who was a member of the victorious 2005 USA Walker Cup team. 'Matt played unbelievable in the morning so I can't really say that I played bad, but I did give him a couple of holes early and he capitalized and got me pretty far down.'
The other semifinal match was a seesaw affair with neither player ever leading by more than 1-up. Watabu bogeyed the fourth to fall 1-down, but the match was even three holes later when Feenstra tripped to a bogey on the par-4 seventh.
Watabu, 22, birdied the par-5 ninth to take his first lead. Feenstra birdied the next two holes to turn a 1-down deficit into a 1-up lead.
However, he bogeyed the 12th and the match was all even again. Watabu birdied 14 to again go 1-up. Feenstra, though, drained a downhill, 10-foot birdie putt on the par-4 18th to force the match into extra holes.
Feenstra was lying four and was still not on the green on the 20th hole when he conceded the match to Watabu, who was on the green looking at a birdie putt.
'My ball striking has gotten better as the week went on,' Watabu admitted. 'I guess it's just up to my putter. I've just got to make some putts out there tomorrow.'
One of the oldest United States Golf Association events, the U.S. Amateur Public Links Championship is being held for the 81st time. The 36-hole final is slated to begin at 10:30 a.m. ET.