A Unification Ministry official said the dozen waitresses and their manager had been "released into society" last week.
They had all been working at a North Korea-themed restaurant in China. Their arrival in the South in April made headlines as the largest group defection for years.
While Seoul said they fled voluntarily, Pyongyang claimed they were kidnapped by South Korea's National Intelligence Service (NIS) and waged a vocal campaign through its state media for their immediate return.
They are then sent to a resettlement centre for three months' training, after which they are free to start new lives in South Korean society.
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Arguing that the high-profile nature of the restaurant workers' case made them unusually vulnerable, the NIS had announced in June that they would remain in protective custody rather than being sent to the centre.
Now that they have been released, the unification ministry said it would provide no further details of their situation "for safety reasons".
The dispute over the defectors has fanned inter-Korean tensions that have been running high since the North's fourth nuclear test in January.
Nearly 30,000 North Koreans have fled poverty and repression at home to settle in the capitalist South.
But group defections are rare, especially by staff who work in the North Korea-themed restaurants overseas and who are handpicked from families considered "loyal" to the regime.
The South's government estimates that Pyongyang rakes in around USD 10 million every year from about 130 restaurants it operates -- with mostly North Korean staff -- in 12 countries including neighbouring China.
A group of liberal South Korean human rights lawyers -- having gained power of attorney from the relatives -- forced a court hearing into the case in Seoul in June.
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