LSU went ahead 3-0 early but Ben Tate ran for a touchdown to give Auburn a 7-3 lead.
Before halftime, Jarrett Lee was intercepted by Gabe McKenzie, who returned it for a 14-3 lead.
Andrew Hatch was knocked out of the game and Lee returned, connecting with Chris Mitchell on a 55-yard touchdown. Keiland Williams threw a TD to Demetrius Byrd for a 17-14 LSU lead.
LSU added a field goal but Chris Todd threw a late TD pass to Robert Dunn for the lead.
Lee threw game-winning touchdown to Brandon LaFell with 1:03 left to play.
First LSU win at Auburn since 1998.