Stuart Moore and Jonathan Dismuke came through with Auburn's best scores with Moore at an even par 70 and Dismuke finishing +2.
"Right now, I am really pleased," Auburn coach Mike Griffin said. "I wish we could have had a few strokes better, but I am real proud of the effort by Stuart Moore and Dis(Dismuke). Those were two good rounds."
Florida leads the pack at six-over-par 286, one shot ahead of Georgia. Clemson and Georgia State are tied at third with 288 totals while Penn State (290), Georgia Tech (291) and Rhode Island (292) lead the Tigers.
Dismuke opened his round with birdies on holes six, seven and 15, but five bogeys on the back nine left the Auburn senior with a 72 score.
Moore opened with back-to-back birdies before a double bogey on the fourth and a bogey on the seventh put him at +1. Despite bogeys on 14 and 17, Moore rebounded on the back nine with three birdies to finish with 70.
"For most of the day the two of them combined were under par," Griffin said. "They came in over par, but they did a good job of carrying their weight around the golf course."
Will Claxton and Matthew Myers had troubles on the front nine posting rounds of 75 and 77 while seven bogeys, two doubles and a birdie gave Andrew Medley an 80.
"In these conditions, I am figuring that's probably where everything is supposed to be," Griffin said. "We will have to play a little bit better tomorrow to set up that final round coming up."
Auburn's Thursday morning tee times were delayed an hour because of fog. The Tigers are scheduled to start at 11 a.m. CDT on Friday with Claxton leading off at 11:51 a.m.