During the Battle of White Oak Swamp in June 1862, Lewis was struck in the right leg by a fragment of an artillery shell. He later participated in all the 5th Regiment's battles with the exception of Mine Run and Antietam until May 1864, when his left arm was amputated at the shoulder as a result of injuries he suffered during the first day of the Battle of the Wilderness. He was then transported to Fredericksburg, and then Buffalo, where his wife tended him during his convalescence. In September 1864, he was honorably discharged, and joined the Veteran Reserve Corps (VRC) as a colonel; in March 1865, he was promoted to brigadier general.