The Hatters were paced by senior Sam Ryder, who finished 21st overall in the field with a five-over par score of 221 at the 6,934-yard Links at Stono Ferry.
Stetson had team scores of 308, 303 and 311 over the three rounds.
Florida raced away from the field for a 15-shot team victory over the two-time defending national championship team from Augusta State. The Gators finished at 20-under par as a team with a total score of 844.
The Hatters will be back in action in two weeks at the Bash at the Beach Tournament, hosted by Appalachian State in Myrtle Beach, SC. That event will be played on March 12-13 with practice rounds scheduled for Sunday, March 11.