He was severely wounded in his ankle in a skirmish at Ruff's Mill on July 4, 1864, during the Atlanta Campaign and, as a result, had his left leg amputated. Three months later, Maj. Gen.Joseph Hooker assigned Noyes, who was still recuperating and using crutches, to the command of Camp Dennison near Cincinnati, breveted him as a brigadier general. Noyes commanded the post until April 22, 1865, when he resigned to become city solicitor.
He was elected in October 1866 as the probate judge of Hamilton County.
He was elected to the governorship in 1871, besting another former Union Army officer, Col. George W. McCook, by more than twenty thousand votes. He served one two-year term between 1872–74, pushing for stricter coal mine inspection laws and promoting fish conservation. He lost re-election in 1873 by 817 votes, 50.1% - 49.9%.
He later served as Rutherford B. Hayes's Minister to France from 1877 to 1881, a patronage reward for his strong support of his fellow Buckeye soldier during Hayes' presidential campaign.