The Italian was sent to the stand after arguing with referee Martin Atkinson over what he perceived as time-wasting by Arsene Wenger's men.
Di Canio said after the match that he had invited the sending off from Atkinson by stating to the official: "If you want to complete a perfect job, you can send me off. He took it seriously and sent me off."
The Football Association confirmed on Monday that Di Canio had been charged and will have until September 19 to respond.
"Paolo Di Canio has been charged by The FA over an alleged breach of FA Rule E3 in relation to behaviour that amounted to improper conduct during his side's game against Arsenal on Saturday 14 September 2013," the governing body stated on their website.
On what was a controversial afternoon at the Stadium of Light, Di Canio was also angered after Jozy Altidore's goal was ruled out.
Atkinson brought play back after blowing for a foul in the build-up to the goal.
The defeat left Sunderland bottom of the Premier League with just one point.
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