Auburn Athletic Director Jay Jacobs welcomed back Malzahn, who was the Tigers' offensive coordinator from 2009-11 and played a key role in helping them claim the 2010 national championship behind quarterback Cam Newton.
"Coach Malzahn was the clear unanimous choice of our search committee, and I am pleased that (president) Dr. (Jay) Gogue has accepted our recommendation," Jacobs said. "This is a great day for Auburn football and Auburn University."
Malzahn's direction of the Tigers' powerful offense in 2010 earned him the Broyles Award recognizing the top assistant coach in college football, but he will inherit a program that has fallen far in two years.
The Tigers this season posted a 3-9 mark -- including 0-8 in the SEC -- leading to the firing of Coach Gene Chizik.