The Underwater Demolition Team member was brought to the surface unconscious after working 24 meters deep in search of the missing seamen, a Defense Ministry official said.
Frantic rescue efforts have been hampered by murky water and strong currents at the site, which lies just south of the disputed border and within range of North Korean artillery.
Fifty-eight crew members were rescued before the ship snapped in half and sank on Friday night.
Early reports that the North may have been involved rattled financial markets but South Korean officials later said there was no clear indication Pyongyang had played a part.
South Korea's defense minister said on Monday nothing had been ruled out as a possible cause, including the chance the ship was struck by one of the thousands of sea mines laid by North Korea during the 1950-53 Korean War.
President Lee Myung-bak visited the site of the rescue operation on Tuesday about 170 km from the west coast port of Incheon. Lee ordered vigilance against the North.
North Korea has made no mention of the sinking in its official media but issued a warning on Monday about moves by the South and the United States it said could lead to unpredictable incidents.
