Led by freshman Glenn Northcutt and sophomore Jay Moseley, who shot even par rounds of 72, the Tigers finished at 293 in round two. That gives them a two-day total of 588, five strokes below the cut that will be made after Friday's round.
UNLV and Coastal Carolina are tied at 583 for 15th place. The Washington Huskies overtook day one leader Wake Forest with a six-under-par total to move into first place at 13-under-par 563, three shots ahead of the Demon Deacons and Arizona State.
Florida is fourth at seven-under-par to lead the SEC teams in the event.
Northcutt overcame a double bogey and bogey on four and five to turn at one over par. After a bogey on 10, he finished the back nine with six pars and two birdies.
Moseley opened with three bogeys and one birdie on the front nine and reverse that after the turn with three birdies and one bogey to finish square with par.
Andrew Medley actually had the best start for the Tigers, but finished with the third best score at 74. He turned at one under par with one bogey and two birdies, but on the backside he slipped with one double bogey, two bogeys and a birdie.
The Tigers counted a 75 from Patton Kizzire, who had three bogeys and 15 pars. He had a par on every hole on the back nine.
Stuart Moore's round of 77 wasn't counted for the team score. He led the Tigers in day one with a 72.
"We played better than the first round, but we still need to improve more," said Auburn coach Mike Grififn.
"We are only five shots off the cutline but there are a lot of teams bunched up that we need to jump. I am happy with the way that we hung in there, but we need to dig a little deeper if we are going to move up. We need a total team effort from all five guys."