The program planned several activities to honor Manning, who set or tied 47 school records during his time at Ole Miss and was later selected No. 1 by the then-San Diego Chargers in the 2004 NFL draft and then traded to the New York Giants.
Both end zones in Vaught-Hemingway Stadium were painted "MANNING."
Manning's nephew and coveted quarterback prospect, Arch Manning, was in attendance. Ole Miss is one of a handful of teams Arch is considering. He has also visited Alabama, Georgia and Texas.
ESPN ranks Arch, a five-star prospect, as the No. 1 quarterback in the 2023 class.
Manning led the team through the Walk of Champions prior to the game on Saturday. Ole Miss coach Lane Kiffin wore Manning's New York Giants jersey.
Manning twice won the Super Bowl and was named to the All-Pro team four times during his pro career. His No. 10 jersey was retired by the Giants earlier this year.
Manning became the third Ole Miss player to have his number retired by the school, joining his father, Archie Manning (18), and Chucky Mullins (38).