With the outbreak of the Civil War and Virginia's secession, Jones resigned his commission in the United States Army on May 27, 1861 to enter the Confederate service as a captain of artillery. He was appointed a colonel of infantry and served in what became the Army of Northern Virginia. He participated as a staff officer in Stonewall Jackson's Shenandoah Valley Campaign of 1862, Front Royal, the Seven Days Battles, the Second Battle of Bull Run, Fredericksburg, and Chancellorsville. In May, Jones was promoted to brigadier general in Edward "Allegheny" Johnson's division to replace John R. Jones (not related). During Johnson's assault on Culp's Hill at Gettysburg, Jones suffered a severe wound to his thigh that put him out of action. Some sources say that it was a head wound, but in his official report, Jones cites extreme hemorrhaging of his thigh. In August, Robert E. Lee called Jones "a good commander" when he assigned him to lead the brigade vacated by William "Extra Billy" Smith, who had returned to Virginia as governor. Late in the year, Jones was wounded again during the Mine Run Campaign.