Hamilton struck the first pitch he saw from Ian Kadish (Blue Jays) -- a fastball into center field -- then scored from third on a wild pitch by Kadish (0-1).
Batting leadoff and playing center field, Hamilton, whose main purpose in the AFL is honing his defense at a new position, made outs in his other four at-bats, dropping his early batting average to .276.
He did not steal a base Wednesday, leaving him with six swipes through eight games. He would need to pick up his pace to reach the AFL record of 24 steals, set by the Javelinas' Rickey Holifield in 1994.
Trayce Thompson, the White Sox's top-ranked prospect, hit his first Fall League home run, a solo shot for the Rafters, in the eighth. Thompson, who entered the game 2-for-19 at the plate over his first six games, also singled in a run during the sixth-inning rally.
Javelinas starter Robbie Erlin was long gone by that point. The Padres' No. 8 prospect gave up a run on one hit over three innings.
Rafters counterpart Andre Rienzo, Chicago's 18th-ranked prospect, was charged with two runs on four hits -- and five walks -- over 4 2/3 frames.
The Rafters advanced the game-tying run to third base in the ninth, but Javelinas reliever Kevin Quackenbush (Padres) struck out Matthew Skole (Nationals) to end the threat. Quackenbush earned his fourth save in his sixth appearance.
Andrew Pentis is a contributor to MLB.com and writes the Prospective Blog. Follow him on Twitter at AndrewMiLB. This story was not subject to the approval of Major League Baseball or its clubs.