Athletic director Jay Jacobs declined to say who else he interviewed, but said it didn't matter.
"The characteristics that he brought to the table were head and shoulders above everybody else," Jacobs said.
Before his arrival at Auburn in 2009, Malzahn had spent two seasons as Tulsa's offensive coordinator. He was the offensive coordinator at Arkansas for one year after a successful run in the Arkansas high school ranks.
Auburn had the nation's 115th-ranked offense last season, averaging 305 yards a game. The Red Wolves were ranked 19th in total yards under Malzahn.
"We will be a fast-paced, attacking-style offense and defense," Malzahn said. "In this day and age, I believe you have to."
It's the second straight time Auburn has turned to one of its coordinators from an unbeaten team. Chizik ran the defense for the 13-0 team in 2004 but was hired by the Tigers despite a 5-19 record in two seasons at Iowa State.
"We are tremendously excited that Gus Malzahn will be our next head football coach," Jacobs said. "Coach Malzahn was the clear unanimous choice of our search committee, and I am pleased that Dr. Gogue has accepted our recommendation. This is a great day for Auburn football and Auburn University."
The search committee was comprised of Jacobs, Auburn Heisman Trophy winners Pat Sullivan and Bo Jackson and former Tigers player Mac Crawford.
Jackson said he was confident that "we got the right man."
"We talked to a lot of talented coaches, a lot of coaches that are going to be Division I coaches other places, and they're all stars in their own right," said Jackson, the 1985 Heisman winner. "Gus shined a little bit brighter than those guys in the interview process."