Following the Kentucky Campaign from June to October 1862, Stovall was ordered to join Gen. Braxton Bragg's Army of Tennessee, and fought during the Battle of Stones River from December 31 to January 2, 1863. He was promoted to the rank of brigadier general on January 20, 1863. His brigade was assigned to Maj. Gen. John C. Breckinridge's Division in D.H. Hill's II Corps from June 6 to November 12. His brigade participated in the Siege of Jackson in Mississippi on May 14.