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.
Jones rejoined the army during the Maryland Campaign and took command of the Stonewall Division, leading it in capturing the Union outpost at Harpers Ferry. At the Battle of Antietam, he was stunned by a shell burst. Though not actually wounded, he was forced to relinquish command. Following the Maryland Campaign, he was tasked with rounding up deserters in the Shenandoah Valley.
Jones rejoined the Army of Northern Virginia the day before the Battle of Fredericksburg, when he returned to command his old brigade. After Fredericksburg, charges of cowardice were levelled against him by several subordinates, who claimed he had used a tree for protection. He was again charged with cowardice for leaving the Chancellorsville battlefield because of an ulcerated leg. He was never given a field command again and was seized by Federal troops on July 4, 1863, in Tennessee. He was imprisoned for the rest of the war with no desire by Richmond authorities to affect an exchange.
After the war, he was a businessman and a minor office holder in Harrisonburg, Virginia.
- Sifakis, Who Was Who in the Confederacy.
- John R. Jones at Find a Grave Retrieved on 2009-03-22