Coach Mike Griffin's Tigers, who qualified for the event as the number two team at the NCAA East Regional, made a good start on the opening round and were challenging for the lead after nine holes. However, they never recovered from a back nine collapse that led to a 295 opening day round.
The Tigers improved by four shots to 291 on Thursday and were four strokes better again on Friday, but that put them at a 33-over-par 873, one shot behind New Mexico.
The cut line was 851 and the leader, Stanford, goes into the final round with a 12-under-par total of 828, two shots ahead of Coastal Carolina. UNC-Charlotte and Alabama, which are tied for third place, are 10 shots off the pace.
The bright spot for the Tigers on Friday was a two-under-par round of 68 by Andrew Medley, which ties the third lowest round in school history in an NCAA championship event. With rounds of 73 and 74 the first two days, Medley ended the day in 74th place individually.
"I played well today," Medley said. "I got off to a good start. I turned at four-under, but gave some back on the back nine. Overall, I played pretty good today. It is bittersweet. I am glad I played well and ended my college career with a good round, but I wish our team had done better for the week."
Glenn Northcutt hits a chip shot on Friday.
Auburn's coach noted he was surprised at the result. "I just wouldn't have dreamed us playing like this on this golf course," Griffin said. "I am proud of the way our lone senior, Andrew Medley, finished his college career. He had a very good tournament and had an outstanding final round.
"We just didn't have it as a team this week," Griffin said. "We had played so well heading into the championship. It is tough knowing how well we have been playing to the way that we finished. We had two bad holes on the first day and never recovered from that."
Sophomore Glenn Northcutt finished tied for 92nd with a 217 total after a second straight round of 71. Junior Patton Kizzire is tied for 127th with rounds of 73-72-77--222 and juniors Steven Groover (77-74-73--224) and Jay Moseley (74-75-75--224) are tied for 137th.