At the outbreak of the war, Johnson enlisted in the service of the Confederacy. He reached the rank of brigadier general by February 1862. He fought at Fort Donelson, Shiloh, Perryville, Stones River, Chickamauga, and Knoxville. Promoted to Major General in 1864, Rust commanded the section of trenches where the South Carolinian troops were at the Crater. He retreated the siege with Confederate forces involved at White Oak Road / Lewis's Farm and Five Forks before his division was crushed at Sailor's Creek and forced to surrender without a command at Appomattox Courthouse.