Auburn shot a second straight round of nine-over-par 293 at Ohio State University's Scarlet Course on Friday, which puts the Tigers in a tie with Stanford, two shots behind co-leaders South Carolina and UNLV.
The top five teams in the 13-team regional advance to the nationals in Atlanta. Auburn is just one shot ahead of top-seed New Mexico along with Texas Tech, which fired the low round of the day with a score of 288.
Missouri is in seventh place at 595, nine strokes behind Auburn.
First round leader Charlotte struggled in round two, shooting a 309, dropping into a tie for eighth place with San Francisco, one shot behind Missouri.
Freshman Jake Mondy led the Tigers on Friday with a one-under-par round of 70. He turned at plus two after back-to-back bogeys at eight and nine, but responded with three straight birdies to open the back nine. He wrapped up his round with five pars.
Michael Johnson shot a 73 for the Tigers while Dominic Bozzelli finished at three-over-par 74.
Michael Hebert continued his struggles with a 76 after shooting 78 on Thursday. Dominic Bozzelli also shot 76 for the Tigers.
Mondy, Bozzelli and Johnson are tied for 10th place individually at 145, five shots behind Carl Jonson of UNLV, who is at two-under-par.