Orren Tims came off the bench to add 17 points for the Lumberjacks (22-8), who never trailed and will play Texas A&M-Corpus Christi in the semifinals Thursday.
Marquez Haynes, the Southland Player of the Year, led the Mavericks (16-14) with 17 points.
After trailing 33-20 at halftime, Texas-Arlington pulled to within 10 points, but Williams later drilled three straight 3-pointers to give Stephen F. Austin a 52-27 lead. Williams was 5 of 7 from 3-point range.
Stephen F. Austin, the defending tournament champion, led 29-9 early due largely to Tims, who came in after starting center Jereal Scott got into early foul trouble. Tims had 15 points at halftime.