Scotland Yard said a suspect is being held at a police station on suspicion of causing a public nuisance. The eight competitors in the final were apparently unaffected, and many said they didn't know about the bottle until being told about it by reporters afterward.
"I just heard about it. I didn't actually see it," gold medallist Usain Bolt of Jamaica said. "I don't promote violence. Sorry to hear that."
Police said the 40-year-old man was heard shouting abuse before he threw the bottle. His name was not immediately released.
It landed on the track about 10 metres behind the runners, who were already in the starting blocks. The bottle bounced a few times and came to rest in the lane occupied by Jamaica's Yohan Blake, who finished second in the race.
"I was so focused, I didn't see anything," Blake said.
Edith Bosch of the Netherlands, who won a judo bronze medal earlier in the games, wrote on Twitter that she was in the stands and that "a drunken" fan threw the bottle. Security was seen rushing toward one section of seats just after the 100-meter final started.
"There was a little distraction," said American bronze medallist Justin Gatlin. "I didn't know what it was. But when you're in those blocks and the whole stadium is quiet, you can hear a pin drop, literally. So you just have to block it out and go out there and do what you have to do. You can't complain about that. The race went on. It was a great race."