Stanford (196.6), Michigan (196.425) and Illinois (195.8) failed to make the cut.
The Utes seemed in shock they failed to qualify as they watched the final competitors from their vantage point by the vault.
"It just wasn't our night," Utah senior Mary Beth Lofgren said. "I am still proud of the team, we just didn't do a good enough job."
The Utes, who won the Pac-12 title and the regional title, had a lackluster opening on the uneven bars to fall behind early, but the biggest surprise was their finish, or lack of it.
The Utes were in fifth place with a 98.25 at the halfway mark. Florida (98.925), Alabama (98.725), Nebraska (98.55), and UCLA (98.475) were ahead of the Utes while only Penn State (98.1) trailed.
The Utes were in a similar position at the NCAA regional meet, where they went from third to first after a big floor effort, so they knew they were capable of changing their fate with one event.
Unfortunately, they couldn't complete the comeback. Utah scored a 49.475 on the floor, even though the usual rock-steady Georgia Dabritz scored a season-low 9.775.
The score was good enough to move the Utes ahead of Nebraska momentarily with the Huskers scoring 49.1 on the uneven bars.
But in the big twist of the night, Utah managed just 49.3 on the vault and Nebraska rebounded with a 49.45 on the balance beam, scoring four straight 9.9s, to jump back ahead of the Utes with the 197.1.
The Utes thought they were going to spend their final bye watching and hoping UCLA couldn't knock them out with a good final performance on the uneven bars. Instead, the Utes went to their locker room looking shell-shocked at their sudden elimination.
"They deserved it," said Utah coach Greg Marsden. "That was a heck of a beam set. They went to the toughest event and won it."
All year the Utes used their embarrassing ninth-place finish in 2013 as motivation. That they fell short on a night they fully expected to shine seemed incomprehensible.
In the end, the meet came down to some hops on the vault landings as Dabritz, who scored a 9.925, was the only one to stick, Marsden said.
"It's heartbreaking," Marsden said. "They've all worked so hard and for it to end here, this way, really is disappointing. It's hard to swallow."
Even through tears of disappointment, Dabritz tried to be positive. The finish couldn't take away from what the team viewed as a successful year.
"Last night we went over the season and were asked what our favorite moments were and we all had different moments," she said. "We were the first team from our school to win a Pac-12 title and that can't be taken away from us."
The Utes had a lot of great moments, Dabritz said, they just expected to have an opportunity for a few more.
O IN SHORT • Utah's gymnastics team fail to make the Super Six for the second year in a row after a subpar effort on the vault.
KEY MOMENT • Nebraska earns four 9.9s on the balance beam to overtake the Utes.
KEY STAT • The Utes ranked third on the vault with a 49.5 average, but scored a season-low 49.3.