Malzahn was announced as the winner of the award Monday before the Tigers met Florida State for the BCS championship. He was elected in online fan voting and by national media and players and coaches in the College Football Hall of Fame.
Malzahn led Auburn into the title game in his first season after inheriting a 3-9 team.
North Dakota State's Craig Bohl is the FCS coach of the year. Minnesota Duluth's Curt Wiese won Division II honors and Pete Fredenburg of Mary Hardin-Baylor was honored in Division III.
Each coach of the year winner receives a $50,000 donation from Liberty Mutual Insurance to support his favorite charities and a $20,000 donation to his school's alumni association for scholarships.