The team announced Tuesday that Shortell will transfer from Minnesota.
"Max is an outstanding young man, and I respect and understand his decision to transfer," coach Jerry Kill said in a prepared statement. "I will help him in any way I can and wish him all the best as he continues his education and football career elsewhere."
Shortell started two games in 2011 and three games this season in place of MarQueis Gray before suffering a left arm injury Oct. 13 against Northwestern. Minnesota then went with Nelson, considered by many to be the team's quarterback of the future. Nelson started the Gophers' final six games.
Shortell completed 65 of 116 pass attempts for 853 yards with six touchdowns and five interceptions this season. He led the Gophers to wins against Western Michigan and Syracuse but struggled in Big Ten games against Iowa and Northwestern. He played sparingly in Minnesota's final two games.
Without Shortell, Minnesota will use Gray, who is now primarily a wide receiver, as Nelson's backup for the Meineke Car Care Bowl of Texas. True freshman Mitch Leidner is also on the roster, and the Gophers have secured a verbal commitment from quarterback Chris Streveler for the 2013 class.