Jones was a native Virginian and a graduate of the Virginia Military Institute. At the outbreak of the Civil War, Jones raised a volunteer company, the Rockingham Confederates, which became Company I, 33rd Virginia Infantry. He began his career as captain of that company and fought at the First Battle of Manassas. In early 1862, he was promoted to lieutenant colonel of the 33rd. He fought in General Thomas J. "Stonewall" Jackson's Shenandoah Valley Campaign in the spring of 1862 and was appointed to command a brigade in the Stonewall Division. He commanded the brigade throughout the Seven Days fighting at the Battle of White Oak Swamp and Malvern Hill, where he was wounded.