When the Civil War broke out, Reverend Jones enlisted as a private in Company G of the 22nd Georgia Infantry on August 4th 1861. Company G, known as "The Fireside Defenders", was organized by William's older brother, Robert Harris Jones at Silver Creek near Rome, Georgia and became it's Captain. On November 16th 1861, William was elected to the position of regimental chaplain. He served with the unit until transferring to the Phillips Legion's Cavalry Battalion in November of 1863. He remained in this position until surrendering with the Battalion on April 26th 1865 at Greensboro, North Carolina.
William returned to Georgia after the war and died at Milledgeville after a lengthy illness on July 9th 1900.