Auburn dropped three spots in the fourth and final round on Friday and finished ninth, 27 strokes off the pace set by Southern Cal, which led from start to finish.
Danielle Downey is in line to earn All-America honors as a senior.
Downey tied for sixth place with a 12-over-par 300 total, three shots off the pace set by Mikaela Parmlid of Southern Cal, who was medalist after taking a one-hole playoff victory over Andrea Vander Lende of Florida. Downey shot a 74 in the final round.
Downey has been plagued with wrist problems this season. However, she carded her third strong finish at the NCAA Championship. She was second last year and fourth in 2000 as a freshman. Downey wrapped up her college career with the second best career stroke average in school history.
"We just didn't have it during this national championship," Auburn coach Kim Evans said. "Danielle, Diana (Ramage) and Celeste (Troche) each had an outstanding tournament. There is nothing to be ashamed of finishing in the Top 10."
Celeste Troche shot a 75 on Friday to finish at 303 in a tie for 19th place. She became the only four-time All-American in Auburn history and set school records for career stroke average (74.2), single-season stroke average (72.45 in 2000-2001), most sub-par rounds (34) and low 54-hole score (210).
Ramage tied for 11th with 301 total after shooting a 74 on Friday with four birdies. She bounced back from an opening day 81 to score an even par 72 and a pair of 74s the next three rounds.
Freshman Maria Martinez shot a second straight 81 and finished at 323, which tied her for 101st. Kingsley Barrett shot an 83 in the final round to finish at 333, which was 120th.
For the Tigers, it was a fourth straight finish in the Top 10 at the NCAA Championship despite not having a single round when they were able to count four strong scores. Auburn tied for second place last season, finished fourth in 2001 and sixth in 2000.
Auburn shot a 304 on Friday following rounds of 317, 303 and 300. Southern Cal won with rounds of 305, 303, 293 and 296.
Pepperdine, which shot 1,212 was second place, 15 strokes behind Southern Cal. The Waves were followed by Texas (1,213), Ohio State (1,214), UCLA (1,216), Oklahoma State (1,216), Arizona (1,217), Florida (1,221), Auburn (1,224) and Duke (1,225).
Georgia was 11th at 1,226 and was followed by host Purdue (1234), North Carolina (1,241), California (1,242), Vanderbilt (1,242), Stanford (1,245), South Carolina (1,248), Arizona State (1,250), Florida State (1,256), Kent State (1,256), Tulsa (1,257), Nebraska (1,281), Washington State (1,288) and Wisconsin (1,291) in the 24-team event.