Jones was an Athletic Coaching Education major and a member of the Athletic Director's Academic Honor Roll. As a freshman in 2002, Jones appeared in 11 games for West Virginia as a reserve cornerback and safety. He totaled one interception and one forced fumble with 36 tackles. During 2003, he appeared in all 13 games, starting nine at cornerback, and taking over full-time kick return and punt return duties. Jones' second season resulted in a second team All-Big East Conference selection with his career-high 89 tackles and four interceptions, one being for a touchdown. He also had six tackles for losses, one forced fumble and two fumble recoveries. He also had a career-high 12 passes defended that season. In a game against Boston College, Jones scored two touchdowns in a 35–28 win over the Eagles, one an 87-yard kick return and the other, a 47-yard interception return. Jones also had a career-high 12 tackles against Miami. Jones totaled 98 punt return yards on 16 punt returns and 867 kick return yards, including an 87-yard touchdown return.