Green fired a second-round best 78, matching her first-round total, to jump from a tie for fourth place after Round 1 to win.
UAB's Brooke Mangan's rounds of 77 and 81 were good enough for second place, two shots behind Green. Suzanne Jepson of South Alabama and Shelley McGraw of Birmingham-Southern, finished third and fourth, respectively, with two-day totals of 159 and 160, also respectively.
JSU won the individual title by eight shots over UAB, who finished second after winning the first-ever Southern Shootout last year. Southern Miss was five strokes behind the Blazers in third, Troy State finished fourth and Tennessee Tech rounded out the top five.
Jacksonville State's Marilen Fernandez-Ruiz shot 163 for the two rounds to finish in a five-way tie for fifth with Troy State's Tracy Tidwell and Allyson Wills, Nicholls State's Shawna Frazer and Kayla Bowsher of The Citadel. Shannelle Howell and Marie-Eve Dion of Jacksonville State were 10th and 11th, respectively.
Birmingham-Southern finished seventh behind Gardner-Webb, who leap-frogged the Panthers after round one. Samford finished eighth behind Kelly Villarreal, whose 172 was good enough for a tie for 19th overall.