Biles, 24, will no longer compete in Sunday's vault and uneven bars finals, USA Gymnastics announced in a statement on Saturday.
"Today, after further consultation with medical staff, Simone Biles has decided to withdraw from the event finals for vault and the uneven bars. She will continue to be evaluated daily to determine whether to compete in the finals for floor exercise and balance beam," the statement read.
"MyKayla Skinner, who had the fourth-highest score in vault during qualifications, will compete in vault finals for the U.S. alongside Jade Carey, who finished with the second-highest score," gymnastics officials said.
Had she competed on Sunday, Biles could have attempted the Yurchenko double pike in Olympic competition and would've been able to defend her title from the 2016 Rio Games.
Her decision to withdraw comes days after she unexpectedly bowed out of the women's gymnastics team final on Tuesday night, partway through the competition, and then said she would not appear in Thursday's individual all-around final.
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Biles cited both her mental health — in particular, the rattling stress of this particular competition, in which she was the face of Team USA — and the sudden onset of what she called the "twisties," when she lost her ability to sense her body move in the air.
"For anyone saying I quit. I didn't quit, my mind & body are simply not in sync as you can see here," Biles wrote on social media on Thursday. "I don't think you realize how dangerous this is on hard/competition surface nor do I have to explain why I put health first."
In their statement on Saturday, USA Gymnastics said "we remain in awe of Simone, who continues to handle this situation with courage and grace, and all of the athletes who have stepped up during these unexpected circumstances."
Biles had been set to compete in the individual finals for vault, beam, uneven bars and floor, which start on Sunday.
USA Gymnastics told PEOPLE in a statement Tuesday evening that Biles had "withdrawn from the team final competition due to a medical issue. She will be assessed daily to determine medical clearance for future competitions."
After Biles' withdrawal from the all-around, officials said the exit was "in order to focus on her mental health."
On Tuesday night, Biles told reporters she was "just dealing with some things internally which will get fixed out in the next couple of days," adding that she was worried her stress would negatively impact her performance and her team's chances to medal.
Biles also told Today's Hoda Kotb that she was "going to take it day by day and we're just going to see."
The decorated athlete thanked her friends and fans on Thursday after she spoke about her mental health concerns and why she chose to withdrawal.
"The outpouring love & support I've received has made me realize I'm more than my accomplishments and gymnastics which I never truly believed before," Biles wrote on Twitter.
Simone Biles / Instagram
With Biles, who was the defending champion, not competing in Thursday's all-around final, her spot went to fellow American gymnast Jade Carey. The 21-year-old from Arizona missed the finals by one spot due to her ninth-place finish, while Biles had finished in first.
Carey and Sunisa Lee, who placed in third at qualifying, represented the U.S.
Lee, an uneven bars powerhouse, won gold and became the fifth consecutive American female gymnast to win the all-around title (which Biles won in 2016 in Rio). Carey finished in ninth place.
Biles, who was seen cheering for Carey and Lee at Thursday's final, on Friday shared clips of herself practicing on the bars, which will be the first apparatus to hold an event final, on Sunday.
To learn more about Team USA, visit TeamUSA.org. Watch the Tokyo Olympics now on NBC.