According to police, the Alabama fan shot the Auburn fan outside of an Extenda Suites motel around 7 p.m. on Monday.
"The male subject got mad, pulled out a firearm and struck the victim in the thigh and fled," the police report said.
Mobile Police arrested 28-year-old Rodney Alexander on Thursday night on a charge of first-degree assault.
The victim's condition was unknown as of Thursday afternoon.
No. 1 Alabama and No. 6 Auburn are set to play in the rivalry game known as the Iron Bowl on Nov. 25.
The winner will move on to play in the SEC championship game the following weekend and with a win could find itself with a spot in the College Football Playoff.