In the first Cowboys playoff win since 1996, playing against the Philadelphia Eagles in the NFC Playoff Wild-Card game, Jones led the team with 16 carries for 148 yards (including a 73-yard touchdown run) and a 30-yard reception. His 148 yards are the third-most rushing yards in a playoff game in team history and his 73-yard run is the longest in franchise postseason history. Jones also became the first NFL player with 400 rushing yards on fewer than 50 career carries since Bo Jackson did it in 1987.

In the 2006 season, Jones rushed for 1,168 yards and scored six touchdowns on 154 carries, thus averaging 8.7 yards per carry. He was also an all-American kickoff returner and had one touchdown on a 100-yard kickoff return against Ole Miss, and caught 15 passes for 107 yards and three touchdowns. Jones alongside McFadden and Peyton Hillis, it was the first time in University of Arkansas history that two different running backs rushed for more than 1,000 yards in the same season. Jones was a second-team All-SEC by the conference’s coaches, and second-team All-SEC by the media. That team finished 10-4 and won the SEC Western Division title.

In 2010, Jones bulked up to 225 pounds in order to improve his durability and was officially moved to the top of the depth chart at running back. He rushed for 109 yards on 15 carries against the Tennessee Titans, for his first 100-yard game. He played in all 16 games for the first time in his career, starting seven games together or in place of Barber and leading the team with 800 rush yards on 185 carries (4.3 yards average) and a touchdown. Against the New York Giants he had the longest reception in his career (71 yards).

In 2011 after Barber was released by the Cowboys, the expectation was that Jones would be the primary running back. He also slimmed down into the 210-215 pound range, in order to regain some of the explosiveness he lost in the previous year. After suffering a left high ankle sprain in the fifth game of the season against the New England Patriots, the four games he missed gave rookie DeMarco Murray the opportunity to earn the starter position. Against the Giants, Murray was lost for the year when he broke his ankle in the first quarter, giving Jones a chance to rush for 106 yards and have six receptions for 31 yards. He rushed for 108 yards on 22 carries, and added three receptions for 23 yards against the Tampa Bay Buccaneers. He finished the year with 585 rushing yards on 127 carries (4.6 average) and 33 receptions for 221 yards.

On May 14, 2013, Jones signed a one-year contract with the Philadelphia Eagles who were looking for him to backup LeSean McCoy and Bryce Brown. After being passed on the depth chart by Chris Polk, he was traded to the Pittsburgh Steelers in exchange for linebacker Adrian Robinson on August 23.