Mr Pence is in Pyeongchang to cheer on American athletes, but he is also warning the world against falling for the glossy image of the two Koreas as they march in the opening ceremony under one flag.
Moon met and shook hands with Kim who serves as the first vice director of the Central Committee of the ruling Workers' Party of Korea of the DPRK.
The North's high-ranking delegation, including the younger sister of its leader Kim Jong Un, will meet Moon and have lunch with him on Saturday.
Saturday's meeting was the first time a South Korean president hosted North Korean officials at the Blue House since November 2007, when late liberal President Roh Moo-hyun, the political mentor of Moon, invited then-North Korean premier Kim Yong Il for lunch following a meeting with government officials in Seoul.
Pence and the North Korean delegation, who both attended the Games opening ceremony, had no contact with each other.
U.S. Vice President Mike Pence and his wife were seated beside the Moons and next to Japanese Prime Minister Shinzo Abe and his wife. But privately, officials said, Pence expressed concern to Moon about his more conciliatory tone toward North Korea. During the parade of nations, they stood only for the US team.
The Hwasong-14 ICBM, successfully tested twice a year ago, also made its first appearance at the parade.
In a meeting hours before Friday's opening ceremony, Abe warned Moon not to fall for North Korea's "smile diplomacy" during the Olympics, according to Moon's office.
The pranksters made their appearance as war threatens to break out between the US, North Korea and South Korea.
"The simple truth is that the time has come for North Korea to permanently abandon its nuclear and ballistic missile ambitions - to recognize there is no future as a member of the family of nations for a nuclear-empowered North Korea", he said after touring the Cheonan naval memorial, a tribute to the South Korean ship sunk in 2010.
Later, Moon watched the joint Korean women's ice hockey team - the first ever combined team at the Olympics - take on Switzerland, joining Kim Yo Jong and Kim Yong Nam, the North's nominal head of state, who is also visiting the South for the Games.
The North has sent almost 500 people to the Pyeongchang Games, including officials, athletes, artists and also a 230-member state-trained cheering group after the Koreas agreed to a series of conciliatory gestures for the games.
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