Hooker, who played in three games in 2012, was sidelined by concussions last year as well.
He will remain in school on a medical scholarship, school officials said.
Who will fill the spot now is something the coaches must still hash out, said a discouraged coach Kyle Whittingham.
The Utes didn't have much depth at the position to start, and now it's looking even thinner.
"It's something we're going to have to talk about," Whittingham said.
The most likely candidates are Quade Chappuis, Tyron Morris-Edwards or Charles Henderson in the role.
Chappuis, a senior, played in five games in 2012 before a shoulder injury ended his season. Morris-Edwards is a onetime walk-on who has continued to improve after playing in nine games last year. Like Morris-Edwards, Henderson is a receiver turned defender.
The 5-foot-9 sophomore played mainly on special teams last year, but has a lot of talent, Whittingham said.
Still, a lack of experience at the position is bothersome, although weighing most on Whittingham's mind Thursday was the loss of Hooker.
"The overall concern is for his health," Whittingham said of Hooker.
More injury news
Sophomore running back Jarrell Oliver left practice early after injuring his left foot, the same one that hampered him last year. Senior Brian Blechen is only at "60 percent," in Whittingham's estimation as he continues to deal with lingering injury issues. Blechen does have a redshirt year available, but Whittingham said the coaches haven't reached the point where they might discuss redshirting him this year.
"If it gets much further down the road, it's something we have to take a look at," Whittingham said.
This and that
Offensive lineman Carlos Lozano, who has struggled to reach a playing weight, has left the team. ... Thursday was the team's best day so far, with Whittingham noting quarterback Travis Wilson and linebacker Gionni Paul had standout days. Paul, who transferred from Miami, will redshirt this year unless NCAA sanctions against Miami allow transfers to play immediately.