With the BeachBoys trailing, 4-3, Giants prospect Roger Kieschnick led off the ninth and reached first after swinging at a wild third strike. Two outs later, Smith lined a 1-2 pitch from Phillies' former first-round pick Kyle Drabek (1-2) over the center field fence.
A 23-year-old Cubs third base prospect, Smith was mired in a 3-for-18 slump. But he'll get to play for his second championship in three months after winning a Florida State League title with the Daytona Cubs.
Waikiki (19-17) finished 1 1/2 games in front of Honolulu (17-18) in the East Division and will play the West Oahu CaneFires on Sunday for the HWB crown.
Jeremy Papelbon, another Cubs prospect, allowed back-to-back singles leading off the bottom of the ninth. After a sacrifice bunt, Hawaii native Kala Ka'aihue (Braves) was intentionally walked to load the bases. But Papelbon, the younger brother of Boston Red Sox closer Jonathan Papelbon, retired Phillies farmhand Michael Taylor on a pop-up to second base and Darin Holcomb (Rockies) on a fly ball to center to notch his league-leading seventh save.
Damon Sublett (Yankees) and James McOwen (Mariners) delivered RBI singles for Waikiki.
Dodgers farmhand David Pfeiffer (1-0) worked around a leadoff walk in the eighth to pick up the win. BeachBoys starter Waldis Joaquin (Giants) gave up three runs on five hits with a walk and a strikeout in 1 2/3 innings.
Smith's homer was the only hit allowed by Drabek in 4 1/3 innings. The 20-year-old right-hander retired 10 of the first 11 batters he faced, fanning five, after tossing six scoreless frames in his last appearance.
Sharks starter Scott Shaw (Mets) allowed three runs on two hits and two walks with two strikeouts over four-plus innings. The 23-year-old right-hander retired the first eight hitters before yielding a two-out single in the third.
Dominic Brown (Phillies) went 3-for-4 to finish the HWB season with a .389 average. Lars Davis (Rockies) homered and scored twice and Jim Rapoport (Cardinals) contributed two hits and an RBI for Honolulu (17-18).
Steve Conley is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.