Davis played football for coach Ben Schwartzwalder at Syracuse University from 1959 to 1961, and went on to national fame in each of those three seasons, twice winning first-team All-American honors. As a sophomore, Davis led the 1959 Syracuse team to a national championship, capping an 11–0 season with a 23–14 win over the Texas Longhorns in the 1960 Cotton Bowl Classic, where Davis was named Most Valuable Player. That same season, Elmira "Star-Gazette" sports writer Al Mallette coined the nickname for Davis, the "Elmira Express". In his junior year, 1960, he set a record of 7.8 yards per carry and was the third leading rusher in the country with 877 yards, having rushed for 100 yards in six of nine games. The 1960 Syracuse Orangemen finished with a record of 7–2 and did not play in a post-season bowl game. In Ernie's senior year, the 1961 Orangemen finished with a record of 8–3, closing the season with a 15–14 victory over the Miami Hurricanes in the Liberty Bowl, played at Philadelphia's Franklin Field. College football used limited substitution rules at the time and players played both offense and defense.