Jones missed the entire 2012 offseason workouts because of shoulder surgery and failed the conditioning test at the start of training camp. Used in a change-of-pace back role, Jones' best game came against the eventual Super Bowl champion Baltimore Ravens, when he replaced an injured Murray and finished with 18 carries for 92 yards and one touchdown. After playing in all 16 games and having seven starts, he battled through knee injuries to finish with 664 yards from scrimmage and a career-worst 3.5 yards average per carry. The Cowboys decided not to re-sign Jones after the season, making him a free agent. During his five years with the team he registered 2,728 rushing yards, with a 4.8 yards average and 11 touchdowns, while also adding 1,062 receiving yards with three touchdowns.