The Tigers, who entered day two of the four-day tournament in second place, dropped to 19th place after shooting a 27-over-par total of 315 on Wednesday after posting a one-over-par 289 total on Tuesday.
Only 12 of the 24 teams in the field were able to complete their rounds after play was stopped for a second time due to winds that were gusting up to 60 miles per hour.
"We finished our round and had a tough day," Auburn coach Kim Evans said. "We got off to a bad start and actually played better as the wind picked up. Play was suspended and we lost about five shots on the last few holes."
Southern California and UCLA are tied for the tournament lead at eight-over-par, 20 shots ahead of 10th-ranked Auburn at the University of New Mexico Championship Golf Course.
Cydney Clanton led Auburn with a 75 and fellow freshman Sarah Thead checked in at 78. Margaret Shirley, who was one-under-par on day one, shot an 80 on Tuesday. Candace Schepperle, who led the Tigers with a 69 in round one, shot an 82 on Wednesday as did teammate Mariana Macias.