The quartet of senior Adam Brown, junior Karl Krug, junior Drew Modrov and senior Kohlton Norys swam a time of 2:49.95 in the final relay to beat Florida's relay team by almost two seconds.
"This is the way this meet is supposed to be," Coach Brett Hawke said. "The SEC is an extremely tough conference and Florida always gives us a run for our money. We have a tough team and winning the SEC title is a part of who we are. We have a tradition of excellence and this is an amazing team. I couldn't be more proud of their fight and will to hold on in the end."
The Tigers celebrate their SEC Championship on Saturday night at the O'Connell Center in Gainesville, Fla.
For the host Gators it was the 10th year in a row they finished as the runnerup to the Tigers. The margin of 17 points is the closest between first and second during that stretch.
The top individual performance by an Auburn swimmer on Saturday came from Arianna Vanderpool-Wallace, who set an NCAA record in the 100-yard freestyle in the prelims and matched the time of 46.81 in the finals. Vanderpool-Wallace broke the eight-year-old NCAA record of 47.00 held by Olympian Natalie Coughlin.
"It feels great to swim that fast," Vanderpool-Wallace said. "I wanted that record for so long. I kept looking at the records board in Auburn and knew I wanted my name up there. Now it's there and I'd like to keep it for a while."
Arianna Vanderpool-Wallace celebrates her NCAA record time in the 100-yard freestyle on Saturday.
Despite Vanderpool-Wallace's efforts Auburn finished third in the women's competition with 563 points. Georgia repeated as champs with 720 points and Florida was second with 678.
"There isn't much to say except that she is a phenomenal athlete," Hawke said after Vanderpool-Wallace was named the SEC Women's Swimmer of the Year. "She is one of those athletes that come along once every 10-15 years. She loves to compete and hates to lose. She continually wants to be better at everything she does."
Senior Dan Mazzaferro was named the top diver and Auburn's Jeff Shaffer was named the diving coach of the year for a fifth straight season.
In the men's competition, Florida took the lead to open Saturday night's competition with a good showing in the 1650 freesstyle. Freshman Zane Grothe took fourth place for the Tigers in the 1,650.
The Tigers immediately responded to the challenge with Brown winning the 100 freestyle and three teammates scoring in the championship heat.
Brown's winning time of 41.92 is the fastest this season for a college swimmer. "Adam has taken another step towards becoming one of the fastest swimmers in the world," Hawke said. "He proved that this week by putting himself above the rest. I'm really proud of him and am expecting big things come NCAAs."
Junior Karl Krug was third in the event recording a career-best time of 42.78. Freshman Marcelo Chierighini was fourth in 42.82 while Modrov was seventh in 43.34.
The Auburn women's team of Hannah Riordan, Caitlin Geary, Emily Bos and Vanderpool-Wallace captured the 400 free relay title.
Senior diver Dan Mazzaferro was named SEC Male Diver of the Year and was one of two to take the men's SEC Commissioner's Trophy. Diving coach Jeff Shaffer was named the SEC Men's Diving Coach of the Year for the fifth-straight year.
The women will compete at the NCAA Championships March 17-19 in Austin, Tex., and the men's nationals are march 24-26 in Minneapolis.