Auburn announced the hiring Monday of VanGorder, who has run Atlanta's defense for four years.
VanGorder's move continues his pattern of moving back and forth between college and NFL positions. He is the former coach at Georgia Southern and former defensive coordinator at Georgia, where he won the 2003 Broyles Award as the nation's top assistant coach.
VanGorder left Georgia to become an assistant with the Jacksonville Jaguars in 2005 before coaching at Georgia Southern and moving back to the NFL with the Falcons.
He has been a head coach twice, at Division I-FCS Georgia Southern and at Division II Wayne State.
"This is a tremendous opportunity for me and my family at this point in my career, both professionally and personally, to become the defensive coordinator at Auburn," he said. "I'm looking forward to working at a school with the success and tradition of Auburn, and for a coach like Gene Chizik, who has led the program to a national championship. I'm very appreciative to the Atlanta Falcons and coach Mike Smith for the experience of the last four years. It's a great organization and will have continued success in the future."
The Falcons finished the regular season ranked sixth in the NFL in rushing defense and 12th in total defense. Their season ended with Sunday's 24-2 loss to the Giants in an NFC wild-card game.
"Brian has been an integral part of our success here over the last four years," Atlanta's Smith said. "This is a decision Brian and his family have made and I want to personally thank Brian for all of his hard work and all the work he has done to make us successful here in Atlanta."
VanGorder could be joined in departing Atlanta by offensive coordinator Mike Mularkey, who is scheduled to interview Tuesday for the Jaguars' head coaching job, an NFL source told ESPN NFL Insider Adam Schefter.
Chizik said he targeted VanGorder from the outset to replace Ted Roof, who took the same position at Central Florida. However, Roof confirmed to ESPN.com's Adam Rittenberg on Monday night that he has left UCF to become the defensive coordinator at Penn State. Roof will reunite at Penn State with new Nittany Lions head coach Bill O'Brien, who was introduced Saturday in State College, Pa. O'Brien served as Duke's offensive coordinator under Roof in 2005-06.
"From the beginning of this process, I had one person in mind, and that was Brian," Chizik said. "He has achieved success at every level, both professionally and collegiately, which is a testament to his ability as a coach. He has been one of the best defensive coordinators in the NFL, has won a Broyles Award at the college level, and understands what it takes to succeed in the Southeastern Conference."
The Tigers finished the regular season ranked 78th in total defense and 79th in scoring defense a year after a national title run.
VanGorder had already accepted a job on Steve Spurrier's staff at South Carolina when Smith hired him.
Auburn announced the hiring just 5 hours before rival Alabama faced LSU in the Allstate BCS Championship Game.
Chizik is still seeking a replacement for offensive coordinator Gus Malzahn, who left to become head coach at Arkansas State.
ESPN college football reporter Joe Schad, ESPN.com's Adam Rittenberg and The Associated Press contributed to this report.