On 15 September 1944, U.S. forces landed on Peleliu and on Angaur in the Palau Islands, and on 18 September, with her repairs and overhaul complete, "Ro-41" got underway from Kure to begin her third war patrol, assigned a patrol area in the Palaus east of the Philippine Islands. On 24 September 1944, she received orders to move to the Morotai area. She was east of Morotai on 3 October 1944 when at 08:07 she fired all four of her remaining torpedoes at the U.S. Navy escort aircraft carriers and . "Ro-41"′s crew heard two explosions, and her commanding officer believed that she had sunk one of the carriers and damaged the other. In fact, her torpedoes missed both carriers, although one hit the destroyer escort in the stern.