In April 1863, he was promoted to brigadier general, backdated to November 29, 1862. Wagner commanded the 21st brigade during Maj. Gen. William S. Rosecrans's occupation of Chattanooga, Tennessee, in September 1863. Wagner's 21st brigade was kept as the garrison force in Chattanooga during the battle of Chickamauga. His men suffered heavy losses in an assault on Missionary Ridge during the Chattanooga Campaign. Wagner was again active in the 1864 Atlanta Campaign, commanding the 2nd brigade in the IV Corps, which suffered exceptionally heavy losses at the Battle of Kennesaw Mountain, and a division during the Franklin-Nashville Campaign.