Kim Bo-reum and Park Ji-woo crossed the line almost four seconds ahead of the third Korean skater, Noh Seon-yeong, in the quarter-finals on Monday.
In the pursuit, the clock only stops when the final skater has crossed the line and teams usually finish with all three skaters bunched together.
Television clips showed Noh in tears after the race while Kim and Park appeared to ignore her and walk away with only their Dutch coach, Bob de Jong, offering Noh comfort.
Noh had been hoping to win gold to honour her late brother, former short track world champion Jin-kyu, who died of bone cancer in 2016.
While Kim and Park were being interviewed after the race, Noh walked out of the arena and declined to answer questions.
“Team pursuit results are decided when the last skater reaches the finish line, and that’s the part where we didn’t do well," Kim said.
Park said she "didn’t know Noh was left behind because it was too loud".
As of Wednesday afternoon, more than 500,000 people had signed a petition lodged with the presidential Blue House, calling for Kim and Park to be ousted from the national team.
If a demand receives over 200,000 signatures within 30 days, the Blue House must address the issue. It has yet to give an answer.
"A sportsman who isn't a team player doesn't deserve to be part of the national team," one petitioner wrote.
"It’s truly a shame to see the athletes bully one another, and they represent the Republic of Korea,” another said.
Public anger has yet to subside despite Kim apologising for her remarks at a tearful news conference on Tuesday. At the same news conference, coach Baek Cheol-gi said it was Noh's choice to skate third on the final lap.
However, Noh said in an interview with local broadcaster SBS that she had never volunteered to be the third skater and had prepared to be in the middle.
"(The three of us) practised in different places and didn't really have a chance to see each other, let alone talk about the race", she said.
The issue is the latest setback for the Korea Skating Union (KSU), which has been plagued by allegations of favouritism and physical abuse over the years.
It also came under fire ahead of the Pyeongchang Olympics after Noh almost lost her spot due to an administrative error.
The KSU later apologised for the error.
The South Korean team finished eighth in the women's team pursuit final on Wednesday.
Noh and Kim declined to comment after the race and Park said "I'm sorry".
(Additional reporting by Yuna Park in SEOUL and Jane Chung in GANGNEUNG,; Editing by Peter Rutherford and Ed Osmond)
