In April 1862, Finnegan was appointed as a brigadier general. He commanded the District of Middle and East Florida until after the Battle of Olustee where he was nominally in charge. Then, he was transferred with a brigade of Florida troops to the Army of Northern Virginia in May 1864. He participated in the Battle of Cold Harbor and served with the Third Corps and the Army of Northern Virginia through the siege of Petersburg. On March 20, 1865 he was ordered to Florida, where he finished out the War.