As a junior in 2004, he was the secondary captain and led the team in tackles and interceptions. Jones also played briefly on offense, as well as returning punts and kick-offs for the second season. He was named first-team all-Big East as a defensive back and honorable mention All-American by several sources. He led the team with 76 tackles, adding two sacks, three interceptions, and seven passes defended. Jones was named to collegefootballnews.com's All-American first-team and was named honorable mention All-American at kick returner. Jones was also named Big East Special Teams Player of the Year. His 76-yard punt return against East Carolina was his season-long return and only punt return for a touchdown in Jones' career. Jones ended his college career in the 2005 Gator Bowl, when he fumbled a kick return early in the game; the Mountaineers lost to Florida State.