After the secession of Virginia, Jones recruited a company, soon to be known as the "Washington Mounted Rifles," of which he was elected captain. He served under J.E.B. Stuart at the Battle of First Manassas. Afterward, he was promoted to colonel, in command of the 1st Virginia Cavalry, and later the 7th Virginia Cavalry. In September 1862, he was promoted to brigadier general. In June 1863, he distinguished himself at the Battle of Brandy Station. However, in the course of the offensive into Pennsylvania, he disagreed with Stuart. Soon after, he was reassigned to the Department of Southwest Virginia and East Tennessee. He participated in the Knoxville campaign, and then at the Battle of Cloyd's Mountain. During a raid into the Shenandoah Valley in June 1864, at the battle of Piedmont, he was struck with a minie ball and died instantly.