On January 31, 1865, President Abraham Lincoln nominated Warner for appointment to the grade of brevet brigadier general, Volunteers, to rank from April 1, 1864, "for gallant and meritorious service" at the battle of Spotsylvania Court House, and at the battles of Winchester, Fisher's Hill and Cedar Creek and the United States Senate confirmed the appointment on February 14, 1865. Warner was promoted him to captain, 8th U.S. Infantry, in the Regular Army (United States) on October 8, 1864. He also received brevets as major, lieutenant colonel and colonel, U.S. Army, to rank from March 13, 1865, "for gallant and meritorious service during the war." Warner was appointed brigadier general, volunteers, on May 8, 1865, to rank from May 8, 1865, although his nomination to this grade was sent to the U.S. Senate only on January 13, 1866 and was confirmed by the Senate on February 23, 1866. On July 17, 1866, President Andrew Johnson nominated Warner for appointment to the grade of brevet brigadier general, U.S. Army, to rank from April 9, 1865, "for gallant and meritorious services in the field during the war" and the U.S. Senate confirmed the appointment on July 23, 1866.