The Spaniard has been charged with improper conduct and has until 6pm on January 2 to respond after his outburst.
Emery grew frustrated as Arsenal let a 1-0 lead slip on the south coast, ultimately dropping two points against the Seagulls.
Now he has been punished by the Football Association after booting the bottle at a supporter.
An FA statement read: "Arsenal manager Unai Emery has been charged following the game against Brighton yesterday [26 December 2018]
"It is alleged his action of kicking a water bottle during the fixture amounts to improper conduct.
"He has until 6pm on 2 January 2019 to respond to the charge."
Emery kicked the bottle in frustration and immediately apologised to the fan – and did the same after the final whistle.
Arsenal also gave the supporter Laurent Koscielny’s shirt as a gesture of good will.
Emery could now serve a ban for the incident – much like Jose Mourinho in 2016, when he kicked a water bottle against West Ham.
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