He was commissioned as a brigadier general of volunteers on August 11, 1863. Smith was assigned on March 7, 1864, to the command of the detached division of the XVII Army Corps and rendered distinguished service during the Red River Expedition, protecting Admiral David D. Porter's fleet after the disaster of the main army. During the Red River campaign, he ordered the destruction of the library and other items at Louisiana State University, but the building was spared at the request of Maj. Gen. William T. Sherman, the school's first superintendent. His health failed, and Smith was relieved of field duty on January 17, 1865. After the fall of Mobile, Alabama, he assumed the command of the Department of Southern Alabama and Florida, and then of the Post and District of Maine. He was brevetted as a major general for gallant and meritorious service.