"Injuries are an unfortunate part of the game, and we feel terrible for Zack," Gophers coach P.J. Fleck said in a statement released Saturday.
Annexstad threw for 1,277 yards and nine touchdowns last season as a walk-on freshman. He started Minnesota's first seven games before injuries slowed him down and ultimately ended his season.
He was hurt against Nebraska for what Fleck called an "internal injury in his midsection." An injury that briefly put Annexstad in the hospital.
Sophomore Tanner Morgan figures to start for the Gophers. He stepped in last season when Annexstad went down and threw for 1,401 yards and nine touchdowns.
Minnesota went 7-6 last year and Morgan led the team to a rare win at Wisconsin and a bowl victory against Georgia Tech.
The Gophers open this season at home against South Dakota State on Aug. 29.