The Tigers opened the competition with a round of 274, shot a 292 on Sunday and then posted a 20-over-par 300 on Monday at Prairie Dunes golf course.
"The first 27 holes we played great, we were at nine-under par, and the last 27--it hurts," Auburn head coach Nick Clinard said. "It stings a little bit. It's probably the worst 27 holes in my 13-year coaching career."
Jake Mondy and Matt Gilchrest shot the best rounds for the Tigers on Monday at four-over-par 74. The Tigers also counted rounds of 76 by Niclas Carlsson, a senior in his last college event, and Will Long while Daniel Stringfellow finished the tournament with a 77.
Auburn's 866 team total was 39 shots off the pace set by Stanford, which will go into the match play round as the No. 1 seed. LSU and Alabama tied for second place at four-under-par, nine strokes off the lead.
Gilchrest, a freshman, posted the low three-day score for the Tigers at the nationals with a four-over-par 214. That put him in a tie for 55th in the individual competition. Carlson and Long finished at 217 while Mondy and Stringfellow posted scores of 221.
"They have a lot to learn," Clinard said of his team that featured only one senior. "They have a lot of growing up to do maturity-wise as people and as golfers. This is a good experience for them. They get to realize what they have to work on and what they have to do to improve."
The Tigers, who moved up to as high as second place during Sunday's round two when the team was six-under-par, finished that day in a tie for 11th place at six-over-par.
The cut line for making the match play, which will run Tuesday through Thursday, was five-over-par with SMU and Illinois tying for that position. The other teams making match play include Oklahoma State (even par), Georgia Tech (plus one) and UCLA (plus four).
Stanford's Cameron Wilson won the individual title at six-under-par, winning on the third hole of a playoff vs. Georgia Tech's Ollie Schniederjans.