Marlins starter Austin Brice, Florida's ninth-round pick last summer, struck out six and held the Yankees to a pair of runs on two hits and two walks over five innings for the win in Tampa. Right-hander Luis Gomez worked the final four innings, limiting the New York affiliate to one hit and a walk to earn the save.
The two teams will meet again Wednesday in Jupiter, Fla., to determine the league champion.
Ryan Rieger, the Marlins' seventh-round pick in the 2011 Draft, went 3-for-4 with his first professional home run in the sixth inning en route to scoring four times. The first baseman had batted in only four games for the team prior to the Game 2 breakout.
Jhiomar Veras doubled and drove in three runs, and Yefri Perez knocked home two more for the Marlins, who out-hit the Yanks, 13-3.
The Yankees' only offense came in the fifth when Fu-Lin Kuo was beaned and Henry Pena followed with a two-run homer to left.
Ontario native Evan Rutckyj started for the Yanks and was charged with five runs on six hits and a walk over 3 1/3 innings to suffer the loss. He struck out two.
Game 3 is set for a noon first pitch in Jupiter's Roger Dean Stadium. Fans are not charged for admission to GCL games.