The Runnin' Bulldogs (11-6, 3-1 Big South) trailed by 16 when it opened up the second half by outscoring the Eagles 23-9 with Tyler Strange's 3-pointer pulling them within 46-44. Winthrop clung to the lead until Strange's fifth 3-pointer tied the game at 62 with 1:43 remaining.
Two free throws by Keon Johnson gave Winthrop (7-8, 2-2) the lead again until Hill's basket in the paint and free throw.
Strange finished with 17 points for Gardner-Webb while Tyrell Nelson scored 14 points and grabbed 14 rebounds for his fifth double-double this season.
Winthrop led 37-21 at half after shooting 51.7 percent with Gardner-Webb at 24.2 percent. In the second half, Gardner-Webb shot 50 percent and Winthrop 38.5 percent.