Tookie Brown's jumper at the 4:32 mark pulled Georgia Southern to within 57-54, erasing most of the 16-point lead that South Alabama (6-8, 1-2 Sun Belt) built early in the second half.
The Jaguars scored the next five and the Eagles (4-9, 0-3) went scoreless until Brown's free throws with 23 seconds made it 62-56.
Georgi Boyanov had 10 points and 10 boards for South Alabama. Nick Stover added 10 points and Tafari Whittingham grabbed 10 rebounds. Williams' 3-pointer early in the second half capped a 16-2 run that started before halftime to make it 41-25 for the Jaguars.