He played the halfback position for the Rebels, but handled all of the passing chores. He earned consensus All-America in 1947 when he led the Rebels to a record of 9–2 including a 13–9 win over TCU in the Delta Bowl at Crump Stadium in Memphis, Tennessee. Conerly's 1947 squad had upset wins over Kentucky (14–7 in Oxford), Florida (14–6 in Jacksonville, Florida), LSU (20–18 in Baton Rouge), and Tennessee (43–13 in Memphis). He placed fourth in the Heisman Trophy balloting and was a two-time All SEC performer. He was named Player of the Year and Back of the Year of the SEC in 1947. He set numerous school records and still ranked 12th in 2008 in career total offense with 3,076 yards. He was ranked 12th in career passing with 2,313 yards and 26 TDs.
Conerly also played baseball at Ole Miss, where he hit .467 in 1948 and was offered a professional contract.
Connerly portrayed the "Marlboro Man" in commercials after playing for the Giants.  Conerly and his wife, Perian (author of the book, Backseat Quarterback) retired to his hometown of Clarksdale, Mississippi, where he spent his final days. Conerly owned shoe stores throughout the Mississippi Delta.
Conerly was inducted into the Mississippi Sports Hall of Fame in 1966 and the Ole Miss Athletic Hall of Fame in 1987. He is also a member of the Ole Miss Team of the Century (1893–1992). Conerly is the namesake of the football award, the Conerly Trophy, given annually to the top college player in the State of Mississippi.