With repairs completed, "Sonoma" was recommissioned on 28 September 1863 and assigned to the South Atlantic Blockading Squadron in which she served for the rest of the Civil War. Highlights of this service included her capture on 8 July 1864 of "Ida" a sidewheel steamer which had slipped out of Sapelp Sound, Georgia, and was bound for the Bahamas laden with cotton. In December 1864, Sonoma was part of a Union naval force that landed Union Army troops and a battalion of United States Marines at Gregorie Point near Yemassee, South Carolina, in an attempt to cut the rail line between Savannah, Georgia, and Charleston, South Carolina; they were defeated by a significantly smaller Confederate force in the Battle of Tulifinny.