The Marlins (19-13) erased a one-run deficit with a three-run ninth off of SU reliever Matt Riegler (2-2).
Shenandoah (26-8-1) scored one run in the bottom of the inning and had the tying run at second before reliever Riley Koonce posted the save by inducing two groundouts and a flyout to right.
The VWC rally capped a game in which the two teams traded the lead three times.
Virginia Wesleyan seized early control with four runs in the third before SU responded with one in the third, two in the fourth and three in the seventh to take a 6-4 lead.
The Marlins tied it with two in the eighth with Shenandoah responding with one in the bottom of the frame.
Right fielder Taylor Erby had the big blow for the victors with a two-run double in the ninth.
The Hornets had 10 hits in the contest with John Wilt and Danny Freshley both getting two each.
Designated hitter Nolan Overby hit his team-leading seventh home run of the season with a two-run shot in the bottom of the fourth.
Freshley and Michael Paul both drove in two runs.