The pirate boat came as close as 3km (1.8 miles) to the cargo ship when the navy helicopter arrived at the scene, an official with South Korea's Joint Chief of Staff's office told Reuters news agency.
South Korea said the crew on its warship had received a thank you message from the North Koreans after thwarting the pirate attack.
Seoul did not give any further details about the North Korean vessel or the nature of its cargo.
The South Korean destroyer has been escorting cargo vessels in the region since April.
Last year, pirates attacked more than 100 ships on a key shipping route, demanding huge ransoms for their release.
Their attacks have intensified recently, despite the presence of some 20 foreign naval vessels in the area to counter piracy.
Somalia has been without an effective administration since 1991, fuelling the lawlessness which has allowed piracy to thrive.
When first loaded, the map's focus falls on Somalia where most of the pirates are based. Use the arrow icons to scroll left towards Europe and the United States which are both playing a central role in tackling the problem.
Scroll to the right for a story about the Philippines, which supplies many of the world's mariners.
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