The Hatters (5-10, 3-2 Atlantic Sun Conference) shot a season-high 60 percent from the field (30 of 50), but the Spartans countered by shooting 53.1 percent (26 of 49) and hitting 13 of 28 3-pointers.
With Stetson ahead by eight, USC Upstate (2-13, 1-4) rallied to tie it at 63.
The Hatters regained a six-point cushion, but the lead slipped to one twice, the second time at 72-71 with 28 seconds to go after a 3-pointer by Torrey Craig.
Three seconds later, Stetson's Joel Naburgs made two free throws.
Josh Chavis missed two 3-pointers in the final 15 seconds, the last with 2 seconds to go, as USC Upstate lost its seventh straight.
Craig had 24 points and seven assists for the Spartans and Chavis had 18 points on six 3-pointers.