Funkhouser had 10 strikeouts - including seven in a row - on 80 pitches through seven, but the score was knotted at 0-0.
Funkhouser stayed in to pitch the eighth and ninth innings and conceded two runs in the final frame.
The Bayfield High School standout helped his own cause in the bottom of the inning, however, with a double to spark a three-run, game-winning charge.
Durango High School's Chase Locke walked in the winning run with two outs.