Malzahn said his first priorities will be recruiting and hiring coordinators, but didn't mention any candidates.
Auburn owes more than $11 million in buyouts to Chizik and his coaching staff.
The Tigers are hoping Malzahn can return them to success after a winless SEC season.
"Gus Malzahn is a proven winner," Jacobs said. "He is without question one of the brightest minds in college football and he has won everywhere he has been. Coach Malzahn knows what it takes to build a championship program in the Southeastern Conference. He knows our state and region and he understands what it will take to turn our program around. Coach Malzahn will also be an outstanding ambassador for Auburn University, and that was important to the committee."
The NCAA has been investigating the recruitment of signee Jovon Robinson, who was ruled ineligible after a guidance counselor admitted to creating a fake transcript.
"I feel very confident that everything is fine, and that's my understanding," Malzahn said.
The Tigers badly struggled in a transition to Scot Loeffler's pro-style last season, starting three quarterbacks.
Auburn was ranked in the top seven in rushing, total and scoring offense in 2010 and Newton won the Heisman Trophy in his lone season out of the junior college ranks. It was the Tigers' first national title since 1957.
Without Newton, the Tigers slipped to 100th in total offense in 2011 and then dipped even further.
The defense struggled, too. Defensive end Nosa Eguae said he thinks Malzahn was the right guy.
"I know coach Malzahn, and he's an amazing man," Eguae said. "He's a standup guy. I'm looking forward to the future. I can't wait to get started and turn this thing around and get some wins."