In 1861, Johnson resigned from the U.S. Army to join the Confederate service as colonel of the 12th Georgia Infantry. In December, he was promoted to brigadier general following his service in command at Camp Allegheny. He led the "Stonewall" division in the Valley campaign of 1862 where he was wounded. In February 1863 he received his appointment as major general. He served at Gettysburg, and the Wilderness. At Spotsylvania Courthouse, he was captured, and subsequently re-entered service after his exchange in the Tennessee campaign. He was captured for the second time at the Battle of Nashville but not released until July 1865.