A police spokesman said a man had been heard shouting abuse and was then seen throwing a bottle, which landed behind the sprinters just after the starter told the runners to "set".
The spectator, arrested on suspicion of causing a public nuisance, was removed from the stadium and taken to a police station in east London.
The spokesman said no one was injured during the incident, which did not disrupt the race - the highlight of the athletics programme at the Games - won by Jamaican Usain Bolt.
Edith Bosch, a bronze medal winner in judo at the Games, told Dutch TV she was standing behind the man when he shouted insults at Bolt before hurling the bottle towards him.
The Dutch athlete said she had slapped him around the head before he was taken away by police.
Bolt, who retained his sprint title in an Olympic record time of 9.63 seconds, said he was unaware of the incident.
"I just heard about it, I didn't actually see it," he told a news conference, laughing. "I don't promote violence so I'm sorry to hear that."
