Nelson hit a 10-foot bank shot with 24.3 seconds remaining to put Gardner-Webb (8-10, 1-2 Big South) ahead 54-49. Keon Moore responded with a basket with 14 seconds to again close the gap to three, but Josh Castellanos made a pair of free throws with 12.3 seconds left for the final margin.
Moore scored 20 points and James Bourne 10 for the Eagles (8-7, 2-1). Winthrop, which made 15 3-pointers in its previous game, a victory over Charleston Southern, made only 4 of 20 from long range on Wednesday. The Eagles shot 27.8 percent and missed 10 of their 27 free-throw attempts.
The victory was the first at Winthrop Coliseum for the Runnin' Bulldogs since its first season in the Big South in 2008-09.