Jones quarterbacked Yale to 6–0 and 12–0 victories versus Harvard as a junior and senior, respectively, in 1906 and 1907.

Yale finished with 9–0–1 records both years, and he was named an All-American both seasons.

As head coach, Jones led Yale football to a 5–3–1 record versus Harvard, and gave the most revered pregame pep talk in Yale athletic history before the Harvard–Yale game in 1923.

Before that contest Jones intoned famously, "Gentlemen, you are about to play football against Harvard.

Ducky Pond returned a Harvard fumble sixty-three yards for a touchdown.