At the beginning of the Civil War, Jouett was captured by Confederates at Pensacola but was soon parolled. He then joined the blockading forces off Galveston, distinguishing himself during the night of 7–8 November 1861 in the capture and destruction of Confederate schooner Royal Yacht. Jouett later commanded Montgomery and R.R. Cuyler on blockading duty and in September 1863 took command of Metacomet.
At the Battle of Mobile Bay, 5 August 1864, his ship was lashed to Admiral Farragut’s flagship Hartford, then was sent after two Confederate gunboats. In a short chase Jouett riddled Gaines and captured Selma.
Jouett had other commands ashore and afloat after the Civil War including the North Atlantic Squadron in 1884. In 1889 he commanded a naval force which forced the opening of the isthmus of Panama, threatened by insurrection.
Rear Admiral Jouett retired in 1890 and lived for most of his remaining years at “The Anchorage,” near Sandy Springs, Maryland. He died 30 September 1902.