Hébert was exchanged on March 20, 1862. On May 26, 1862, Hébert was appointed brigadier general. His appointment was confirmed by the Confederate Senate on September 30, 1862. He led a brigade in 1862 at the Battle of Iuka, a division at the Second Battle of Corinth and a brigade at the Siege of Vicksburg (May 18 – July 4, 1863). He was again made a prisoner of war after the Confederate surrender at Vicksburg. He was paroled and exchanged on October 13, 1863. He then served in Confederate operations in the Cape Fear District in North Carolina first in artillery and then as chief engineer of the department. He commanded the heavy artillery at and around Fort Fisher.