Following Johnston's death, command of the Army of Mississippi fell to P.G.T. Beauregard for the Siege of Corinth, where Stewart was present. President Davis soon replaced Beauregard in favor of Braxton Bragg, who transported the army to Chattanooga, Tennessee, in preparation for his invasion of Kentucky. In the Confederate Heartland Offensive, Stewart's brigade fought at the Battle of Perryville in Benjamin Cheatham's division of the army's right wing, commanded by Polk. The Army of Mississippi became the Army of Tennessee near the end of 1862, and Stewart and his brigade served continued to serve in Cheatham's Division in Polk's First Corps at the Battle of Stones River. Stewart was promoted to divisional command and to major general on June 2, 1863, assigned to William J. Hardee's corps for the Tullahoma Campaign. His division unsuccessfully opposed General George Henry Thomas's corps at the Battle of Hoover's Gap before his division was assigned to Simon Bolivar Buckner's corps and fought at the Battle of Chickamauga, Stewart being wounded in the fight on September 19. Prior to the second day, Buckner's corps was assigned to the army's left wing to be commanded by the recently arriving James Longstreet. Following Chickamauga, Buckner was demoted by Bragg and left for Virginia on medical leave; Longstreet left soon after to besiege Union-controlled Knoxville. Stewart's division remained at Chattanooga, and was assigned to John C. Breckinridge's corps, for whom he and his men fought on the extreme left of the Confederate line at the Battle of Missionary Ridge in November 1863.