New Tigers coach Gus Malzahn announced the hiring of the veteran Southeastern Conference assistant Thursday two days after getting the job.
Johnson was fired after Southern Miss went 0-12 in his lone season, but has an impressive track record running SEC defenses.
"Ellis is one of the top defensive minds in all of college football. He is very experienced and has tremendous success coaching in the Southeastern Conference," Malzahn said. "He is a man of integrity who will be a great ambassador for Auburn. We're very pleased to have him join our staff and bring a wealth of knowledge and experience to our program."
His final Gamecocks defense ranked third nationally in yards allowed and second-best against the pass in 2011, his fourth season.
The Tigers had a frequently shuffling lineup on defense last season. They finished 80th nationally in total defense, giving up 420.5 yards a game.
Malzahn told Gene Chizik's assistants on Wednesday that they wouldn't be retained.
Johnson was also head coach of The Citadel from 2001-03. He called his new job "truly a home run for me."
"I'm very fortunate for the opportunity to coach at Auburn and return to the Southeastern Conference, where there is so much tradition and history," Johnson said. "I have a tremendous amount of respect for Gus Malzahn, both as a man and a coach, and I really look forward to working for him."
Johnson has had two stops at Alabama. He was the defensive coordinator and outside linebackers coach from 1997-2000, and his 1999 defense was second nationally against the run and ninth overall.
He coached outside linebackers for the Crimson Tide's 1992 national championship team.