Ashley Gill-Webb, 34, is said to have got past security at the Olympic Stadium into the £750-priced seating area, according to The Sun.
Witnesses have claimed that the vending machine worker began shouting abuse at eventual winner Usain Bolt before throwing the plastic bottle at the race track.
Gill-Webb denied a public order offence while he appeared at Stratford Magistrates Court yesterday.
John Speakman - who was trackside when the incident occurred - said: "The guy had been causing trouble. He appeared to be a chancer who managed to talk his way into that £750 section.
"He kept sitting in different seats and then moving when the real ticketholder came along.
"He ended up among the Dutch athletes which is when he threw a Heineken bottle. The steward then dragged him out towards the police who handcuffed him."
Bronze medallist Justin Gatlin said of the incident: "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."
The race was won by Usain Bolt in a new Olympic Record time of 9.63 seconds.
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