Williamson recovered in time to take part in the Vicksburg Campaign and the following Siege of Vicksburg. After the fall of the city, he assumed command of the 3rd Brigade, 1st Division, XV Corps until September, 1863 then commanded the 2nd Brigade, 1st Division, XV Corps at the Battle of Chattanooga. Williamson's division, commanded by Peter J. Osterhaus was temporarily attached to the forces under Joseph Hooker and took part in the Battle of Lookout Mountain. The division was returned to the Army of the Tennessee and Williamson led the 2nd Brigade during the Atlanta Campaign. At the Battle of Jonesborough he was wounded in the hand. On December 19, 1864 he received a brevet promotion to brigadier general of U.S. Volunteers, on January 13, 1865 a full promotion to brigadier general and on March 13, 1865 a brevet promotion to major general of volunteers. Briefly during the summer of 1865 he commanded the District of St. Louis and was mustered out of the volunteer service on August 24, 1865, but was on an inspection tour of army posts in the West and did not find out until he returned in October 1865.