Coach Matt Wells announced the injury Tuesday afternoon. Keeton sprained an MCL during Saturday's 31-17 loss to Washington.
Sophomore Kent Myers moves up the depth chart after starting five games in 2014.
Keeton played the entire game against Washington, but his movement was visibly limited the previous week against No. 18 Utah.
The senior has battled injuries throughout his career, but his 8,233 career yards of total offense rank No. 2 in school history. He set a slew of school records while leading the Aggies to an 11-2 record as a sophomore, but injuries cut his season short in 2011, 2013 and 2014.
Utah State (1-2) hosts Colorado State on Saturday.