The show of division came on the same day that President Donald Trump announced that he agreed to meet face-to-face with North Korean leader Kim Jong Un.
With spectators packing out the stands and waving the blue-and-white Korean unification flag, teenager Kim Jong Hyon and Ma Yu Chol - who both only started skiing three months ago - were the first over the start line in the cross-country race.
The pair were the first to start at the Alpensia Biathlon Centre in Pyeongchang in a 29-strong field competing in the men's 15km sitting category.
The IPC directed its focus on the achievement of hosting the inaugural North Korean Paralympic team in South Korea despite their history of conflict.
The Paralympic cauldron is lit after the flame arrives in Gangneung, South Korea, on Thursday.
The Winter Paralympic Games have kicked off in PyeongChang.
In an opening address, International Paralympic Committee (IPC) president Andrew Parsons urged the Paralympians to "keep fighting, play fair, have fun and keep pushing your limits".
Among the Americans are 41 returning Paralympians and 33 first-time Paralympians competing in five sports: alpine skiing, Nordic skiing, sled hockey, snowboarding and wheelchair curling.
A record 567 athletes will take part across nine days of competition. At the "Parade of Nations" flag-bearer of the Ukrainian team was the repeated champion and medalist of the Paralympic games in ski racing and biathlon Vitaly Lukyanenko.
Para athletes from Russian Federation are participating in the 2018 Paralympics in the neutral status, or the Neutral Paralympic Athletes (NPA).
The 18-year-old from Vancouver captured bronze on Saturday in the women's standing downhill event with a time of one minute 34.60 seconds at the Jeongseon Alpine Centre, behind victor Marie Bochet of France (1:30.30) and runner-up Andrea Rothfuss of Germany (1:32.53).
North Korea had wanted to use a version of the Korean peninsula flag that includes islands disputed with Japan.
The Opening Ceremony begun with an artistic segment entitled Let's Move, which saw Myeongjin Shin, an amputee performer with a prosthetic arm and legs, beat on a giant drum.