With the outbreak of the Civil War, Polignac initially served on the staffs of generals P. G. T. Beauregard and Braxton Bragg as a lieutenant colonel. He served at the Battle of Shiloh and the subsequent Siege of Corinth. In January 1863, he was promoted to brigadier general. Two months later, he was transferred to the Trans-Mississippi Department and assigned command of a Texas infantry brigade. Polignac is best known for his leadership at the Battle of Mansfield, April 8, 1864, in De Soto Parish, Louisiana, a Confederate victory in the first major action of the Red River Campaign. Polignac received a battlefield promotion at Mansfield to division command after the death of General Alfred Mouton and then proceeded to fight again at the Pleasant Hill, further south in De Soto Parish.