Moon hosted the elderly Kim Yong Nam -- technically the highest-level Northern official ever to go to the South -- and Pyongyang's star representative Kim Yo Jong at the presidential Blue House.
Smiling, he shook hands with each of the delegates ahead of their talks, and television footage showed that Kim Yo Jong -- who analysts expected to bring a personal message from her brother -- was carrying a blue folder emblazoned with a seal.
There is speculation Pyongyang could invite Moon to visit later this year.
The nuclear-armed North's delegation is the diplomatic highlight of an Olympics-driven rapprochement on the divided peninsula.
Tensions between the two soared last year as Pyongyang tested missiles capable of reaching the US mainland and its most powerful nuclear device to date, while Kim Jong Un and US President Donald Trump traded personal insults and threats of war.
The North is subject to multiple rounds of UN Security Council sanctions over its banned weapons programmes. Analysts believe its diplomacy is seeking to weaken the measures against it, and could be trying to loosen the alliance between Seoul and Washington.
Moon shook hands with both Kim Yo Jong and Kim Yong Nam at the Olympics opening ceremony on Friday, and they cheered as athletes from North and South entered the arena together behind a unification flag showing an unbroken Korean peninsula.
US Vice President Mike Pence, who was seated in the same box, did not interact with the North Koreans at any point, US officials said.
He also did not shake hands with Kim Yong Nam while making a brief appearance at a leaders' reception ahead of the ceremony -- although Japanese Prime Minister Shinzo Abe, whose country is also regularly threatened by Pyongyang, did so, while exchanging pleasantries with the North Korean.
"We are determined to make sure that even in the midst of the powerful background & idealism of the Olympics, the World is reminded of the truth about North Korea," Pence tweeted on Friday.
He also reiterated the Trump administration's stance that the US would take whatever "action is necessary to defend our homeland", including military operations, as it seeks to denuclearise the North.
"We're going to continue to put all the pressure to bear economically and diplomatically, while preserving all of our military options to see that that happens," Pence told NBC.
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