The statement said the North Korean ship had sent a message of thanks to the South Korean warship, but did not say when the incident took place.
"The pirates came close to the North Korean ship but retreated as our helicopter approached," a South Korean military spokesman told the AFP news agency.
It was the second time that the South Korean unit has reported driving off pirates since it deployed last month in the sea lanes off Somalia.
A South Korean helicopter drove pirates away from a Danish-registered ship on April 16, the military said.
Peace deals scrapped
The incident comes amid increasingly tense relations between North and South Korea amid rows over the North's nuclear weapons programme and its recent controversial rocket launch.
The North announced earlier this year that it was scrapping all peace pacts with the South.
North and South Korea remain officially at war having never signed a peace treaty ending the 1950-53 Korean War.
Pyongyang thanked the United States, its traditional enemy, in November 2007 for helping the crew of a North Korean ship which was attacked by pirates off Somalia.
But relations have soured considerably since, with North Korea walking out of nuclear disarmament talks and announcing plans to resume its atomic weapons programmes.