Pettus and his command took part in the 1864 Atlanta Campaign, fighting in the battles of Kennesaw Mountain on June 27, Atlanta on July 22, and Jonesborough from August 31 to September 1. Beginning on December 17, he temporarily led a division in the Army of Tennessee. During the 1865 Campaign of the Carolinas, Pettus was sent to defend Columbia, South Carolina, and fought at Bentonville from March 19–21. Pettus was wounded in this fight, hit in his right leg during the battle's first day. On May 2 he was paroled from Salisbury, North Carolina, and, four months after the Confederacy surrendered, Pettus was pardoned by U.S. President Andrew Johnson on October 20.