The Tigers shot a three-under par 277 for the best round on Sunday and finished six-under par with a score of 834 for the weekend. Alabama shot a 282 on Sunday, finishing 12-under par for the tournament with a three-round score of 828. Florida finished third with a three-day total of 841.
"We played very well today," Auburn coach Nick Clinard said. "The first 12 holes we kind of got it rolling. We missed a few putts, but we got to within one shot with five holes to play.
"I think the story of the week for us was we just couldn't close," he said. "We pressed too much. Our short game isn't as good as it needs to be. We have to make more putts to win championships."
In a tie for eighth place on the leader boards after two rounds, Blayne Barber shot a three-under par 67 in the third round to move into a three-way tie for third place with a three-round score of 206. Barber's round was highlighted by an eagle on the par-5 7th hole and a birdie on the par-4 13th.
Alabama's Justin Thomas claimed the individual title with a three-day score of 203.
Sitting at three-under par after two rounds, Auburn's Michael Johnson shot a two-over par 72 on Sunday to finish tied for 7th in individual standings with a score of 209.
After starting the third round in a tie for 30th on the leader board, Dominic Bozzelli shot an even-par 70 to finish in a tie for 15th place for the tournament. Bozzelli shot a 71 and 72 in the first two rounds and ended up at three-over par for the tournament with a score of 213.
Will McCurdy, who was tied for 8th after two rounds, struggled on Sunday, shooting a seven-over par 77 in the final round to finish tied at 27th with a three-round score of 216.
After carding a 14-over par 84 in the second round, Niclas Carlsson carded his best round of the tournament with a two-under par 68.
Next up for the Tigers are the NCAA Regionals, which are slated to tee off on May 17.