In the spring of 1862, Weitzel received his appointment as a chief engineer in the expedition to capture New Orleans. In August 1862, he was promoted to brigadier general in command of a division at the siege of Port Hudson in 1863. He returned to his position as chief engineer in the Army of the James during the siege of Petersburg in 1864. Weitzel was brevetted major general, and he was assigned to command the XVIII and XXW corps. After the surrender at Appomattox, he remained in service until he mustered out in 1866.