The FA have alleged that Arsenal failed to ensure their fans conducted themselves in an orderly fashion during the match, which ended in a 2-0 victory for Unai Emery's side.
Gary Cooper, 30, from Chertsey, has been charged with common assault and encroaching on to the pitch.
It was in the aftermath of this goal that the fan in question evaded security to run onto the pitch in an attempt to celebrate with the Arsenal players.
An Arsenal spokesman said the club condemned the behaviour of the pitch invader and apologised to Smalling and United.
'We will be working closely with the Metropolitan Police in their investigation. The individual will also be banned from Arsenal matches home and away.
"We encourage all supporters to carefully consider their behaviour, not only at this weekend's Premier League, EFL and FA Cup matches, but at all games in the future".
"This is entirely unacceptable and we strongly condemn both incidents".
The statement continued: "It is essential that all players feel safe and supported every time they go on the pitch and there is absolutely no place for any type of behaviour that puts this at risk".