Williams scored 16 after half as Lipscomb (15-14, 10-8 Atlantic Sun Conference) overcame a 38-36 halftime deficit to hold a slim lead for most of the second half.
Raymone Andrews and Hunter Miller hit 3-pointers on consecutive possessions to bring Stetson (7-23, 5-13) within 73-72, but Martin Smith answered with a 3 before Williams hit two free throws to open a 78-72 lead with 3:49 left.
Willie Green's dunk cut the lead to 79-76 with 35 seconds remaining. But Lipscomb held on as Martin Smith made 4 of 4 free throws over the final 25 seconds and Stetson missed two late 3-pointers.
Martin Smith scored 20 and Malcolm Smith 18 for Lipscomb.
Miller led Stetson with 17 points and Green added 15. Kentwan Smith and B.J. Glasford scored 11 apiece.