Villepigue was initially commissioned as a captain of artillery but was quickly promoted to the rank of colonel in the provisional army and assigned to the 36th Georgia Infantry Regiment. His first notable action was to command the defense of Fort McRee, guarding Pensacola harbor, during the bombardment of November 22, 1861. At the time, his commanding officer, General Braxton Bragg, suggested that for the number and caliber of guns involved, this would surely rank as the heaviest bombardment in the world to date. Bragg praised Villepigue's coolness under fire, even while grievously wounded, and noted that his example caused the troops he was leading—for the most part raw volunteers from Georgia and Mississippi—to fight with the courage of veterans.
General Bragg wrote of Colonel Villepigue that he was, "an educated soldier, possessing in an eminent degree the love and confidence of his officers and men, he had been specially selected for this important and perilous post. The result fully vindicates the fortunate choice, and presents for our admiration, blended in perfect harmony, the modest but heroic soldier with the humble but confiding Christian."
Defense of Fort Pillow
Villepigue was promoted to the staff of General Bragg as chief of engineers and artillery. He moved to Mobile, Alabama, and was appointed a brigadier general early in 1862. General P.G.T. Beauregard, who also held him in high esteem, then moved him to command Fort Pillow, Tennessee. Villepigue recognized the weaknesses of the fort’s location, and made efforts to reduce them, however, they were under fairly constant bombardment by Union gunboats. Ordered to retire by General Beauregard, and to destroy all government property including guns, cannon and ammunition, his men blew up his fortifications and retreated to safety. Nineteen pieces of artillery were left behind.
Brigade commander
Villepigue commanded a brigade at the Second Battle of Corinth in October 1862, in the division of Major GeneralMansfield Lovell, under the overall command of Maj. Gen. Earl van Dorn. He distinguished himself in both the successful opening attack and the covering of the eventual retreat. The arduous nature of the campaign laid him low with a fever, however, and, with the promise of a major general's commission, he was sent to Port Hudson, Louisiana, to recuperate. No sooner had he arrived there than his condition worsened and he died of pneumonia.