With Georgia's admission to the Confederacy, Savannah, under Lieutenant John Newland Maffitt, was commissioned by the Confederate States Navy.

She was attached to the squadron of Flag Officer Josiah Tattnall III, charged with the naval defense of South Carolina and Georgia.

On November 5–6, 1861, Savannah, flying Tattnall's flag, in company with CSS Resolute, CSS Sampson, and CSS Lady Davis, offered harassing resistance to a much larger Union fleet, under Flag Officer Samuel Francis Du Pont, preparing to attack Confederate strongholds at Port Royal Sound, South Carolina On November 7, Savannah fired on the heavy Union ships as they bombarded Fort Walker and Fort Beauregard.

Driven finally by the Federal gunboats into Skull Creek, Georgia, Tattnall disembarked with a landing party in an abortive attempt to support the fort's garrison, and Savannah returned to Savannah, Georgia to repair damages.

Her name was changed to Oconee on April 28, 1863, and in June she was loaded with cotton and dispatched to England to pay for much-needed supplies.