At the outbreak of the Civil War, Jones raised a volunteer company, the Rockingham Confederates, which became Company I, 33rd Virginia Infantry. Initially commissioned as captain on June 22, 1861, he fought at the First Battle of Manassas. On August 21, 1861, 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, under Col. John F. Neff (a Lutheran minister's son and fellow VMI graduate killed in action at the Second Battle of Manassas). Jones was then 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, mustered out and recommissioned.