He will replace Jeff Casteel, who was fired this month by coach Rich Rodriguez.
Yates spent the past two seasons at Boise State as defensive coordinator, leading a unit that was ninth nationally with 31 forced turnovers. He was a defensive back at Boise State from 1996-99 and coached defensive backs from 2003-11.
Yates also spent two seasons at Texas A&M as co-defensive coordinator and secondary coach.
Yates leaves less than a week after Broncos offensive coordinator Eliah Drinkwitz left Bryan Harsin's staff for North Carolina State.