Ashley Gill-Webb pleaded not guilty at Thames Magistrates Court on Wednesday to using threatening words or behaviour with intent to cause harassment, alarm or distress.
The 34-year-old man was granted conditional bail and ordered to stand trial at Stratford Magistrates Court in east London on Jan. 3.
Gill-Webb was arrested after the incident at the Olympic Stadium in August. Dutch judo athlete Edith Bosch intervened after the bottle was thrown and pushed Gill-Webb in the back.
Usain Bolt, who won the race in 9.63 seconds, said he was unaware of the incident. American sprinter Justin Gatlin, who finished third, said he had been briefly distracted.