Ashley Gill-Webb, 34, from South Milford, near Leeds, will appear in custody at Stratford Magistrates’ Court on Monday afternoon.
A police spokesman said he was charged with intentionally causing harassment, alarm or distress under section 5 of the Public Order Act.
Ashley Gill-Webb, who is reportedly a father-of-two and a member of a local football team in South Milford, was arrested after the incident last night at the Olympic Stadium.
Dutch world judo champion Edith Bosch intervened after the incident.
She was standing close by when a green plastic drink bottle was thrown from the stands behind the start line.
Edith Bosch told Dutch television station NOS TV: “I had seen the man walking around earlier and said to people around me that he was a peculiar bloke.
“Then he threw that bottle and in my emotion I hit him on the back with the flat of my hand.
“Then he was scooped up by the security. However, he did make me miss the final, and I am very sad about that.
“I just cannot understand how someone can do something like that.”
Edith Bosch’s involvement was brought to public attention on Twitter, where she wrote: “A drunken spectator threw a bottle onto the track! I HAVE BEATEN HIM… unbelievable.”
LOCOG chairman Lord Sebastian Coe said it was “poetic justice” that the man happened to be sitting next to the Dutch judo star.
He said: “I’m not suggesting vigilantism but it was actually poetic justice that they happened to be sitting next to a judo player.”
He added: “Throwing a bottle on to the field of play is unacceptable. It’s not just unacceptable at an Olympic Games but at any sporting event and anybody who does that will be removed.
“There is zero tolerance for anything like that.”
A man had been heard shouting abuse before the bottle was thrown just as the runners were lined up in the starting blocks.
Speaking after the race, 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.”
Jamaican sprinter Usain Bolt, who won the race, said he had been unaware of the incident.
He said: “No, I keep hearing that. I don’t know who would have done that.”
Fellow Jamaican sprinter Yohan Blake said: “I was so focused I didn’t see anything. I was so focused on just running to the line.”
Justin 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.”
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