The Marlins (8-5-4, 4-2-3 ODAC) scored just 41 seconds into the contest to down Shenandoah (0-17, 0-9).
VWC added insurance goals in the 61st and 76th minutes to provide the final margin of victory.
Hornets goalkeeper Cory Thompson made nine saves in his second start of the season.
Virginia Wesleyan outshot the Hornets 25-3 and had a 14-1 advantage in corner kicks.
Shenandoah will announce its 2017 schedule in January.