The Tigers shot a one-over-par 289 on at the Lake Nona Golf & Country Club course to finish eighth of 27 teams. The top 10 teams from each of the three regionals advance to the nationals, which will be held May 31-June 3 at the Crosswater Golf Course at Sunriver Resort in Bend, Ore.
"It's a great feeling," said Auburn coach Mike Griffin, whose team was disappointed after not qualifying for last year's nationals.
"It's good to get back to the championship. We had the good fortune of playing The Preview in the fall out there (at Sunriver) and that is such an exciting venue in Oregon. We wanted to get back to that place, and I am very excited. We are now tied for the lead at the national championship with 29 other schools."
This will be Auburn's 14th appearance at the NCAA Men's Golf Championship.
The Tigers qualified at 15-over-par with 11 strokes to spare. Auburn shot an 879 and UNLV was the final qualifier at 884, seven strokes ahead of Georgia Southern, Georgia State and Indiana, who were in a three-way tie for 11th.
Wake Forest finished first at even-par 864, one shot better than SEC champion and No. 1 ranked Georgia.
Patton Kizzire led the Tigers on day three with a one-under-par 71. The sophomore posted a pair of birdies on both sides to go with one bogey on the front nine and two on the back nine. He finished at three-over-par for the tournament in a tie for 18th place.
Freshman Glenn Northcutt, who had two birdies and two bogeys, was Auburn's second best performer on Saturday with his 72. He finished the tournament at seven-over-par.
Senior Stuart Moore was steady throughout the event. He finished with a 73 on Saturday to end the tournament five-over-par.
"I am real proud of our team," Moore said. "We played with a lot of heart, and it is just a relief."
Andrew Medley came through for the Tigers on Saturday.
Auburn's fourth and final score that counted on Saturday came from Andrew Medley, who bounced back from poor rounds on Thursday and Friday to shoot a 73. That put him at 15-over-par for the tournament.
Jay Moseley, who had gone into day three one-under-par, struggled on Saturday. He shot a 78 to finish at five-over-par. He had three double bogeys on the back nine on Saturday.
Kevin Chappell of UCLA was the individual winner at five-under-par for three rounds.