The jersey will be part of a package that will include helmets signed by LSU coach Les Miles and former South Carolina coach Steve Spurrier.
The opening bid on the athletic department's auction page will be $7,000 and will close at noon ET Monday.
After the Oct. 10 game, in which Fournette ran for 158 yards and a touchdown, the sophomore said he would auction off his jersey to benefit the victims of the flood that caused the Gamecocks to move their home game to Tiger Stadium.
Players are prohibited from auctioning off their game jerseys, and schools are required to take the names off the backs of any sold jerseys that were worn by players with remaining eligibility.
The NCAA is making an exception for the auction, and LSU spokesman Michael Bonnette said the jersey will remained unaltered, with Fournette's nameplate on the back.
"Having been through a similar situation with my family during Hurricane Katrina when I was 10 years old, this is something I wanted to do to help those in need," Fournette said in a statement. "The generosity of people helped my family make it through Hurricane Katrina. I'm hopeful that the money raised with this auction can make a difference for those flood victims in South Carolina."
The highest price ever paid for a college football player's jersey is believed to be $26,290 for a Notre Dame jersey worn by Paul Hornung and sold in 2010. An Ernie Davis College All-Star Game jersey from 1962 sold in the same auction for $23,900.
Last year, a 1976 Tony Dorsett game-used Pitt jersey sold for $15,180, and a Bo Jackson game-used Auburn jersey sold for $11,042.