Gardner-Webb (18-16) improved to 3-2 on the season against nationally-ranked teams with the win. Adam Izokovic earned his sixth save of the year in the ninth, pitching out of a bases-loaded jam to end the game.
The game marked the first back-to-back losses for Appalachian State (24-7) this season.
The Mountaineers looked poised to come away with a close win after surging ahead in the top of the seventh.
Tyler Tewell started the seventh-inning rally for the visitors, belting a single to right center, and Jeremy Dowdy reached on an error to put runners at second and third. Trey Holmes then ripped a double to left center to drive in both Tewell and Dowdy, putting the Mountaineers on top 3-2.
GWU reliever Mitch Warner came on to get out of the jam, however, getting a ground ball, a pop up to third base and a strikeout to end the frame.
Gardner-Webb responded with one out in the bottom of the eighth, with Benji Jackson and Scott Johnson roping back-to-back doubles to tie the game, 3-3. Johnson's double down the line plated pinch runner Alex Newman, and was the second of six consecutive hits for the 'Dogs in the frame.
Zeke Blanton followed Johnson's double with a single to put runners at first and third, and Ryan Hodge drove in the go ahead run with a sharp single through the right side. Blanton scored on the same play from first, when the throw from right field scooted into the Gardner-Webb dugout to give the hosts a 5-3 edge.
Hodge dashed home from third on a wild pitch for a 6-3 lead to end the scoring. John Harris followed that play with a single up the middle, but was thrown out during the ensuing at bat trying for third on a failed pickoff attempt. Dusty Quattlebaum belted a two-out double to the wall in right center, but was stranded to end the inning.
Izokovic came on to get the first out of the ninth inning, but Appalachian State drew two consecutive walks to bring the tying run to the plate. An infield single by Brandon Burris loaded the bases, but Izokovic got a pop up to left and a fly ball to right to end the game with the 6-3 lead intact.
Gardner-Webb went up 1-0 in the bottom of the first, with Hodge scoring from second on a fielding error with two outs. Hodge singled earlier in the inning.
The Mountaineers rallied to tie the score in the top of the fifth, with Trey Holmes collecting a two-out single - then scoring on a Burris ball to deep left that was jarred loose by the outfield fence for an RBI double.
Quattlebaum roped a two-out double in the bottom of the fifth to break the tie, scoring catcher Harris from first to give Gardner-Webb a 2-1 advantage before Appalachian rallied in the seventh.
Warner (2-1) picked up the relief win, retiring all five batters he faced with one strikeout. Starter Andrew Barnett was strong in a no decision, striking out a career-high eight batters in 6.1 innings of work and allowing just two earned runs.
Hodge led an 11-hit attack by the Gardner-Webb offense, going 3-for-5 with two runs scored and an RBI. The Charlotte, N.C., freshman (Butler HS) is riding a 14-game hit streak, the longest of the season for any GWU hitter.
Quattlebaum (2-for-5, 2 2B, RBI) and Johnson (2-for-4, 2B, RBI) also had multiple hits for the Runnin' Bulldogs.
Tyler Moore (2-1) took the loss out of the bullpen for Appalachian State, allowing four runs on four hits in just 0.1 innings. Moore was one of seven Mountaineer pitchers used in the game, with starter Jamie Nunn allowing just one earned run on four hits in 4.2 innings.
Appalachian State had seven hits in the game, getting a pair from Tewell (2-for-4, run), Holmes (2-for-3, 2B, 2 RBI) and Burris (2-for-4, 2B, RBI).