The Cougars finished fifth with a 194.475.
The result, while not surprising, was disappointing for the Cougars, who were once a regular participant in the NCAA Championships.
The Cougars have made eight appearances in the NCAAs, ranking them 16th nationally for the most qualifications for the event.
The Cougars' best finish was eighth place in 1991 here in Alabama. Since then they have finished ninth in 1994, 10th in 1995, 11th in 2000 and 2005 and 12th in 1992, 1996 and 1998.
This year, the Cougars started the season well, taking second in the Cancun Classic and beating Utah State in the home opener. The Cougars also finished the year winning three of their last five meets.
One of the losses was to Utah, 197.125-195.5, a result that was a sign of things to come for the Cougars as they faced some of the top teams in the nation Saturday.
The uneven bars have been one of BYU's better events this season, with the Cougars scoring above the 49.0 mark five times.
But falls from Eliane Kulczyk (9.225) and Megan Bain (9.125) hurt the Cougars, as they finished with just 48.1.
That mark was the lowest of all the teams in the first rotation, effectively ending the Cougars' hopes of an upset before the meet really got started.
Balance beam, which has been the Cougars' trouble spot, added to their woes again Saturday.
Leadoff gymnast Ashley Follett fell, scoring just 8.925. The Cougars avoided any other falls, but couldn't earn the big scores they needed either and finished with just 48.35.
The Cougars finished strong on the floor, scoring 49.075 with the last five scoring 9.8 and higher.