The top 5 teams earned berths in the National Championships, scheduled for May 26-30 in Toledo, Ohio.
The Jaguars, who began the day 12th, shot 5-under 279, their low round of the tournament by three shots, to finish at 2-over 854.
Central Florida shot 11-under 273 to finish at 34-under 818 and win the regional by 11 shots over South Carolina, Georgia and Arizona. The Gamecocks shot 15-under 269, the low round of the tournament, Georgia shot 272 and Arizona shot 282.
Iowa also qualified for the national championships by shooting 276 to finish fifth at 837, six shots ahead of Georgia State, which shot 281.
Georgia Southern shot 275 and finished 10th at 847.
Arizona's Tarquin MacManus claimed medalist honors, shooting 2-under 69 in the final round to finish at 15-under 298, two strokes better than Central Florida's Brad Schneider, who closed with 63.
Henrik Norlander shot 71 to tie for 23rd at 210 and lead Augusta State.