Ashley Gill-Webb spoke only to deny the charge and confirm his personal details during a brief appearance at Stratford Magistrates Court. He was granted conditional bail with a trial scheduled for Sept. 3.
District Judge Angus Hamilton banned Gill-Webb, 34, of Leeds in northern England, from any Olympic venue and the entire Olympic Park for the duration of the games.
In addition to throwing the bottle, he was charged with using threatening words, disorderly behaviour and harassment.
As he left the court, Gill-Webb — who wore a grey hooded jacket and had an asthma inhaler in his mouth — shouted abuse at waiting reporters.
Sunday's race, won by Jamaican sprinter Usain Bolt, was not disrupted.
Gill-Webb's actions enraged Dutch judo bronze-medal winner Edith Bosch, who was inside the stadium near him. She told Dutch TV she intervened after the bottle was thrown and pushed Gill-Webb in the back, causing her to miss the race.
"I'm not suggesting vigilantism but it was actually poetic justice that they happened to be sitting next to a judo player," said Sebastian Coe, chairman of the London organizing committee.
Police said Gill-Webb is alleged to have also shouted abuse before hurling the bottle just before the race began.
Bolt, the Jamaican sprinter who won the race in an Olympic-record time of 9.63 seconds, said he was unaware of the incident. However, U.S. sprinter Justin Gatlin, who won the bronze medal, said he had been briefly distracted.
"When you're in those blocks and the whole stadium's quiet you can hear a pin drop," Gatlin said, acknowledging he had heard the bottle land. "You can't complain about that, the race went on and it was a great race."