The late-night drama was a fitting end to a day which had begun under the threat of a storm and featured the loss of the face of these Games, tennis player Naomi Osaka.
America's silver team medal means Biles can no longer win six golds here which, added to her haul of four from Rio, would have confirmed her status as the greatest gymnast of all time.
USA Gymnastics said Biles had withdrawn because of a "medical issue", and would be assessed daily.
While she could still, in theory, win five and match the current record, it seems unlikely.
Russian great Larisa Latynina won nine gymnastic Olympic golds in the 1950s and '60s. Only Michael Phelps, with his 23 swimming golds, has won more.
If Biles does win five here she would join four athletes on nine – Latynina, swimmer Mark Spitz and track and field athletes Paavo Nurmi and Carl Lewis.
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Tokyo 2020 Olympics - Gymnastics - Artistic - Women's Team - Final - Ariake Gymnastics Centre, Tokyo, Japan - July 27, 2021. Simone Biles of the United States in action on the vault. (Photo: Reuters)
OSAKA EXITS
Osaka, who lit the Olympic cauldron on Friday to open the Games after a one-year postponement, looked out of sorts and never settled into a rhythm as she lost 6-1 6-4 in the third round to Czech Marketa Vondrousova.
Her departure left Japan without its best known global sporting figure in the Olympics.
It was her first tournament since she pulled out of the French Open in May. The women's tennis tournament has now lost both of its top draw cards after Australia's world number one Ash Barty was beaten in the first round.
While Osaka was out, and Biles diminished, other competitors enjoyed better days.
Japan won their second straight gold in softball, beating the US 2-0, and Brazil's Italo Ferreira and American Carissa Moore overcame challenging conditions in brilliant style to win historic first Olympic surfing gold medals.
In the women's triathlon, Flora Duffy, 33, achieved instant national hero status when she won Bermuda's first Olympic gold medal.
With about 63,000 residents, the British Overseas Territory in the North Atlantic Ocean became the smallest nation to win a Summer Olympic gold medal.
In the pool, Russian Evgeny Rylov broke a US stranglehold on the men's 100m backstroke, while Tom Dean powered to gold in the men's 200m freestyle, heading a British one-two with Duncan Scott taking silver.
For Vietnam, its biggest medal hope today, female weightlifter Hoang Thi Duyen was not able to win a medal in the women's weightlifting competition under 59 kg.
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Weightlifter Hoang Thi Duyen competes at the Tokyo 2020 Olympics on July 27, 2021. (Photo: AFP/VNA)
In the snatch event, Duyen registered a starting weight of 95 kg, but it took her two times to lift this weight. On her third try, the athlete decided to raise the weight to 98 kg but she failed to make it and ended at the 4th place in the event.
In the clean and jerk event, Duyen started with 113 kg and she succeeded in the first attempt. But when raising the weight to 119kg, she failed in both the second and third attempts. As a result, she only reached a total of 208 kg, ranked 5th overall.
Meanwhile, both badminton star Nguyen Tien Minh and swimmer Nguyen Huy Hoang also failed in their respective events.
Minh bid farewell to Tokyo 2020 after losing 14-21, 18-21 to Adel Resky Dwicahyo of Azerbaijan in the second round of men’s singles.
Hoang finished second in the second heat of the men's 800 m freestyle after 7:54.16, only ranked 20th out of 34 swimmers, with 16 best performers progressing to the final.
Hosts Japan sit atop the medal tally with 10 golds (18 total), followed by the US with nine golds (25 total), and China in third place having nine golds (21 total).
