Sebastian Coe, chairman of the London organizing committee, said there would be "zero tolerance" for anti-social behaviour.
"Throwing a bottle on to the field of play is unacceptable, it's not just unacceptable at an Olympics Games but at any sporting event and anybody who does that will be removed," he said.
Coe said there was some "poetic justice" involved because the suspect had been sitting next to a judo star who hit him after he allegedly threw the bottle Sunday night. Coe cautioned, however, that he was not supporting a vigilante response.
The man, identified as Ashley Gill-Webb, 34, was charged Monday with a public order offence and was to appear later in custody at Stratford Magistrates Court. He was charged with intentionally causing harassment, alarm or distress, police said.
Dutch judo star Edith Bosch, who won a bronze medal, told Dutch TV she acted out of disappointment and anger. She said she had seen the man acting oddly before the race began.
"I had seen the man walking around earlier and said to people around me that he was a peculiar bloke," she said. "Then he threw that bottle and in my emotion I hit him on the back with the flat of my hand."
Police said the man had allegedly shouted abuse before hurling the bottle just before the race began.
Usain 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 a bit distracted when the bottle was thrown.
"But when you're in those blocks and the whole stadium's quiet you can hear a pin drop," Gatlin said, adding that he did not think the race had been affected.