Chizik had sandwiched two 8-5 seasons around the national title, but never approached the success of 2010, when Newton won the Heisman Trophy. The Tigers were 7-17 in SEC games outside of 2010 during his tenure.
His hiring was criticized by some fans after Chizik went 5-19 in two seasons at Iowa State and lost the last 10 games of his first head coaching job.
Jacobs was heckled at the airport after making the hire.
Chizik had been defensive coordinator on unbeaten teams at Auburn and Texas.
A search committee comprised of former Heisman Trophy winners Pat Sullivan and Bo Jackson and former Tigers fullback Mac Crawford will assist Jacobs, the school said.
A transition year might have been expected.
Chizik had to replace the offensive and defensive coordinators after last season. Chizik made an ill-fated switch from Gus Malzahn's no-huddle, spread offense to a pro-style system with the hiring of former Temple offensive coordinator Scot Loeffler.
The Tigers struggled in the transition, partly because of shaky quarterback play and ended the season with freshman Jonathan Wallace under center.
Auburn ranked at or near the bottom of the SEC in every major statistical category offensively and defensively.
Chizik's tenure was marred by off-the-field problems, too, to the extent that he had employees of a private firm run curfew checks on players this season.
Four members of the 2010 national championship team were arrested on robbery charges in March 2011. Antonio Goodwin was convicted in April and sentenced to 15 years in prison. Dakota Mosley, Michael McNeil and Shaun Kitchens are awaiting trial.
Two-time 1,000-yard rusher Mike Dyer transferred to Arkansas State with Malzahn after being indefinitely suspended before the bowl game.
Freshman quarterback Zeke Pike was arrested in June for public intoxication and later dismissed from the team. Starting center Reese Dismukes was suspended for the opener against Clemson following a public intoxication arrest.