Twelve days later,
Seal was en route back to Fremantle. She arrived on
2 October and departed again on
24 October to patrol in the shipping lanes in the
Palau area. On
16 November, she intercepted a convoy of five cargomen in two columns with a
destroyer escort and conducted a submerged attack on the leader of the near column as the formation zigzagged toward the submarine. Less than a minute after firing,
Seal collided with, or was rammed by, another enemy ship. The
periscope went black and vibrated severely. The submarine rose to 55 feet; hung there nearly a minute then started down. A few minutes later, depth charging began and
Seal leveled off at 250 feet. Breaking up noises were heard. Four hours later, the area was clear and
Seal surfaced. The high periscope had been bent horizontally, and the housing on the low periscope had been sprung, preventing its operation. The radar antenna had been broken off the radio mast. Quantities of uncooked rice and beans, unlike those used on the submarine, were found between the wooden deck pieces of the
cigarette deck, on the bridge, and caught in the
bathythermograph. The
periscope shears yielded "a good sample of Japanese
bottom paint."
Captured Japanese documents later confirmed the sinking of the 3500-ton freighter
Boston Maru by an American submarine on that date in that location. Whether that ship was
Seal’s target or the colliding ship is not known, but it is possible that the freighter's hull had been badly punctured by the submarine's periscope shears.