The man shouted abuse then threw the bottle just as the showpiece final was about to get under way, a Scotland Yard spokesman said.
As the starter called "set" and the athletes rose to wait for the bang, the bottle landed behind the blocks in lane five, a few metres (yards) behind Jamaica's Yohan Blake, who went on to take the silver medal.
It came to a halt just as the sprinters set off.
Blake said: "I was so focused I didn't see anything. I was so focused on just running to the line."
The police spokesman told AFP that the man was arrested inside the Olympic Stadium "on suspicion of causing a public nuisance".
"He had been heard to shout abuse and then threw a plastic bottle on to the track," he said.
"That was immediately prior to the start of the men's 100m final. He remains in custody at an east London police station."
Jamaica's Usain Bolt defended his Olympic title, winning the race in a new Olympic record of 9.63 seconds.
Speaking afterwards, Bolt told reporters he had been unaware of the incident.
"I keep hearing that. I don't know who would have done that," he said.
US sprinter Justin Gatlin, who won bronze, said: "It was a little distraction and 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."
Gatlin said the incident had not affected the race.
"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."