The vice-minister level talks, held on the North Korean side of the border in the jointly-run Kaesong industrial zone, will resume tomorrow morning, Seoul's Unification Ministry said.
"The two sides had a broad discussion of pending issues and exchanged views in a sincere manner," a ministry spokesman said.
The fact that both sides agreed to keep talking will be seen as a positive step for a process that was never likely to produce any substantial breakthrough.
The last such sit-down, with the mandate to discuss a range of inter-Korean issues, took place nearly two years ago.
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Today's talks were the fruit of an August accord that saw both sides step back from the brink of an armed conflict and commit to a process of de-escalation.
"Let's take a crucial first step to pave the way for reunification. I hope various pending issues will be solved one by one," South Korea's chief delegate Hwang Boo-Gi told his North Korean counterpart Jon Jong-Su as they shook hands in the morning.
Jon said the talks were an opportunity to overcome the decades of mutual suspicion and confrontation.
"Let's make efforts to break down the barrier, fill up the cracks and make a new and wide road together," he said.
The elephant in the room for any North-South dialogue is Pyongyang's nuclear weapons programme. But while Seoul was expected to raise the issue of denuclearisation, experts said the two sides were focused on more achievable targets.
"The North's denuclearisation needs to be seen as the ultimate goal of inter-Korea dialogue, not a pre-condition of it," said Kim Keun-Shik, a professor at the University of North Korean Studies in Seoul.