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.

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.

[3] 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.

[4] Formally promoted to major general on June 14, 1864, Polignac led the division throughout the remainder of the campaign and during its service in Arkansas in the fall of 1864.

After the Civil War, Polignac returned to his large estate in France, and resumed his travels and studies in Central America.

In Ober-Ingelheim on 4 November 1874 he married Marie Adolphine/Adolfine Langenberger (Frankfurt, 7 June 1853 – Paris, 16 January 1876) and had one daughter: In London on 3 May 1883 he married secondly Margaret Elizabeth Knight (Olivet, 22 June 1864 – Castle La Roche-Gençay, Magné, 20 August 1940) by whom he also had children: Polignac continued to study mathematics and music until his health failed.