Pence, who arrived at the reception late, left the venue after a five-minute stay, according to pool reports. But Vice President Mike Pence and Kim's sister, Kim Yo Jong were there and sat near one another.
The aide noted that Pence "and our team were aware she'd be in attendance".
Impersonators of US President Donald Trump and North Korean leader Kim Jong-un called for peace at the Winter Olympics just before being thrown out by security. She is also the first member of North Korea's ruling family to visit the South since the Korean War.
Almost 500 North Koreans are participating in the Olympics, which run through to February 25, including a cheering squad, art troupe and taekwondo demonstration team, the South's Unification Ministry said.
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The Korean peninsula has been divided since the 1950-53 war and the two sides have never signed a peace treaty. The North Korean athletes competing at these Olympics are also privileged citizens. "We thank you", he said.
However, the North Korean delegation of political officials will meet with South Korean President Moon Jae-in Saturday.
She is on a U.S. sanctions list over alleged links to human rights abuses in North Korea.
"President Moon and President Trump are completely aligned in their objective for a nuclear free Korean Peninsula", Pence said.
Still, it was widely believed to reflect US suspicions toward the recent rapprochement between the two Koreas. Due to the packed schedule of the Games, that pre-Opening Ceremony primetime coverage was the first time NBC aired competition before the big parade and flag waving in the Olympic stadium.