The bottle struck a Brighton supporter and though it was not included in the official's match report, Emery confirmed he spoke to the fan after the match and apologised for his actions while addressing media after the contest.
"I said to [the supporter], apologies, because I kicked the bottle after a disappointing action for us in the last minutes," he told reporters in his post-match news conference.
"It wasn't hard, but it touched one supporter for them. I said to them 'I'm sorry'."
The Gunners had led in the contest early on through a goal from current Premier League Golden Boot leader Pierre-Emerick Aubameyang.
However, Arsenal were pegged back late in the first half after Jurgen Locadia took advantage of a Stephan Lichtsteiner error to level the procedings and snatch Brighton a point.
A poor second-half display which saw the Gunners barely threaten appeared to leave Emery frustrated, leading him to kick the bottle which ended up in the stands and struck a supporter.
Emery again apologised for the incident at his Thursday news conference, saying that while he hoped he would not be charged by the FA, it was up to their discretion.
The manager has until January 2 to respond to the charge.
The Gunners next travel to Anfield on Saturday where they will face table-topping Liverpool in hopes of inflicting the first Premier League defeat of the season on the Reds.