He again led his division in the Siege of Vicksburg, breaking Confederate control of the Mississippi River. Grant again praised Hovey as key to the siege's success. Shortly after the battle, he received word that his wife had died, and returned home to arrange for guardians for his children. Her death was deeply saddening to Hovey who was slow to recover emotionally. He returned briefly to the front in 1864 to the 1st Division in the XXIII Corps division during the Atlanta Campaign. In August 1864 the 1st Division was discontinued and its regiments dispersed throughout the other divisions in the XXIII Corps. Hovey, without a command, again returned home. For the remainder of the war he was in command of the military District of Indiana. He resigned from the Union Army on October 7, 1865.