Evan Miller got Brayan Morales to fly out with runners on first and third to end the game for his first save of the season.
Hernandez (3-2) allowed four hits while striking out six and walking one to pick up the win.
Fort Wayne started the scoring in the first inning. After hitting a single, Podorsky stole second and then scored on a single by Justin Lopez.
Trailing 5-1, the Loons cut into the deficit in the eighth inning when Carlos Rincon hit a two-run double.
Alfredo Tavarez (0-2) went four innings, allowing two runs and four hits while striking out five in the Midwest League game.
With the win, Fort Wayne improved to 6-3 against Great Lakes this season.
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