[1] He resigned from the U.S. Army on December 29, 1860, a few days after South Carolina seceded from the Union and offered his services to his state's militia.

[1][3] Dunovant held the rank of major of infantry in the South Carolina militia during the initial Confederate operations at Fort Sumter.

[4] On July 22, 1861, he became colonel of the 1st South Carolina Regulars and was stationed for some time on Sullivan's Island and at Fort Moultrie.

[1][4] Dunovant was cashiered and dismissed from the service for drunkenness on November 8, 1862 but on July 28, 1863 he was given another chance to command the 5th South Carolina Cavalry Regiment.

[8][9] Major General Matthew Butler wanted to turn the Union flank and initially rejected Dunovant's insistence on a frontal charge.

[8] Union Sergeant James T. Clancy of the 1st New Jersey Volunteer Cavalry was credited with firing the shot that killed General Dunovant.

"[6] John Dunovant was buried in a family burial plot 3 miles (4.8 km) southeast of Chester, South Carolina.