Once the abandoned Yorktown's crewmen were safely recovered, her escorts departed, leaving behind the destroyer Hughes (DD-410) to keep watch. Early the next day, 5 June, a seaplane from the Japanese cruiser Chikuma spotted the drifting carrier. In mid-morning, Hughes discovered two injured men who had been left behind, rescued them and examined the ship. Later, the tug Vireo (AT-144) came on the scene and took Yorktown under tow, while working parties jettisoned boats and an anchor. However, the old tug could do little more than keep the big ship headed into the wind.

Several other destroyers arrived early on 6 June, carrying a salvage party of Yorktown crewmen. Boarding the carrier at daybreak, the men set to work pushing guns, aircraft and other removable weights over the side, counterflooding to reduce the list and performing the many other tasks involved in saving their ship. USS Hammann (DD-412) lay alongside to provide power, water and other assistance, while other destroyers patrolled nearby to protect Yorktown from intruders.

By mid-afternoon, prompted by the previous day's seaplane report, the Japanese submarine I-168 crept undetected into the area. Taking a submerged attack position, she fired four torpedoes, hitting Hammann and Yorktown amidships on their starboard sides. The destroyer went down in a few minutes. Many of her crew killed or badly injured in the water when her depth charges exploded as she sank. Vireo cut the towline, and the salvage party were taken off the now even-more-greviously wounded carrier. But she continued to float, and plans were made to restart work the next morning.