Born in Rockingham County, Virginia, in the Shenandoah Valley to David Jones and his wife the former Harriet Yost. J.R. Jones had 3 brothers and three sisters. He graduated from the Virginia Military Institute, then became the principal of a military school in Urbana, Maryland. He married Sarah Brashear, one of the daughters of Thomas Cook Brashear of New Market, Maryland, but the couple had no children. Three years before his wife's death, Jones fathered a child with freed slave Malinda Rice, who had begun working in their household at age 16. Jones would eventually acknowledge Marie Magdalene Rice as his granddaughter, as described by her daughter Carrie Allen McCray.
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. 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. Jones healed and rejoined the army during the Maryland Campaign and took command of the Stonewall Division, which then captured the Union outpost at Harpers Ferry. At the Battle of Antietam, his brigade was one of two on the front line and attacked early on September 17. They held the line for about an hour before partially retreating. However, a nearby shell burst stunned Jones and caused hearing loss, so he relinquished his command to Brig. Gen. William E. Starke, who fell mortally wounded, leaving Col. A.J. Grigsby in command. Following the Maryland Campaign, Jones returned to the Shenandoah Valley, and was tasked with rounding up deserters. 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 acquitted in April 1863 after a month-long trial, but 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, near Smithsburg, Maryland. He was imprisoned for the rest of the war with no desire by Richmond authorities to affect an exchange.
Postwar
After the war, Jones became an agricultural merchant, and by 1880 a commissioner of accounts in Harrisonburg, Virginia, the county seat of Rockingham County. Although his only daughter, Mary, was raised by her maternal uncle John and his wife, the general continued to employ Malinda as his housekeeper, and often visited. He bought books for Mary and took her to visit her grandmother Martha in Singer's Glen. When his wife died in 1878, Jones sold his house and moved in with the family of his merchant friend Jonas Lowenbach, and also bought a small house for Malinda and her children. Nonetheless, his acknowledgment of Mary's paternity had social repercussions for both him and his child. The 1900 U.S. Federal Census shows Jones living with 33-year old black female servant Loisa Mills and her three young sons.
Death and legacy
Jones died in 1901 and is buried beside his wife in Harrisonburg's Woodbine Cemetery. His granddaughter's book about her family secret was published in 1998.
