"Throwing a bottle onto the field of play is unacceptable, and it's not just unacceptable at an Olympic Games, it's unacceptable at any sports venue," London organising committee chairman Seb Coe told reporters on Monday.
"The guy was removed and anybody that does that in future will be removed, so there is a zero tolerance to anything like that."
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.
"I am not suggesting vigilantism but it was actually poetic justice that they did happen to be sitting next to a judo player," Coe added.
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."
American athlete Justin Gatlin, who won bronze in Sunday's race, said the bottle had been a "little distraction".
"I didn't know what it was, but when you're in those blocks, and the whole stadium's quiet, you can hear a pin drop," he said.
"You just have to block it out and go out there and do what you got to do. You can't complain about that, the race went on and it was a great race."
Bolt's countryman Yohan Blake, who won silver, said: "I was so focused I didn't see anything. I was so focused on just running to the line."