Gardner-Webb's Tyler Strange made a 3-pointer to tie the game 57-57 with 43 seconds left in regulation.
Hartley hit a 3-pointer for a 62-59 lead in the extra period, and the Bulldogs knocked down 7 of 8 free throws in overtime to claim the victory.
Tashan Newsome scored 14 points and Strange 11 for the Bulldogs (19-11, 10-5 Big South Conference), who have won six straight.
Saah Nimley had 15 points and Paul Gombwer 14 for the Buccaneers (16-11, 11-4), who lost to the Bulldogs 74-73 in overtime in January. Charleston Southern is tied with High Point, which lost to Radford 63-58, in the conference.
Gardner-Webb made 11 of 28 3-pointers to Charleston Southern's 5 of 17.