The Belgium global fell under minimal contact from Hector Bellerin to earn Antonio Conte's side the spot kick which brought them level, just four minutes after Jack Wilshere's 63rd minute opener.
Chelsea's penalty, given for a foul on Eden Hazard by Hector Bellerin, was the right call.
Marcos Alonso thought he had scored the victor on 84 minutes after slotting in Zappacosta's low cross but Hector Bellerin grabbed a late equaliser in the 92nd minute to rescue a point for Arsenal.
Speaking after the game, Wenger told Sky Sports of his disappointment at the decision: "After that, we got again a farcical decision and mentally we were shocked".
Wenger is contesting the FA charge. I am 35 years in football and I know what I said. But Bellerin's late strike denied Chelsea their 11th win in 14 league games and earned Arsenal a deserved point.
The agitated Frenchman will also have to pay a fine totaling £40,000 ($54,225) after being charged by the governing body for his conduct in the match officials' changing room following a 1-1 Premier League draw at West Bromwich Albion on New Year's Eve.
Wenger now has until 6 p.m. on Tuesday to respond. "Both teams had chances that they missed but I think it was a great game of football". "He has to stay calm and continue to play this way, the goals are coming", Conte said.
Arsenal isn't even in City's slipstream but floating far from the leaders, sitting adrift by 23 points and actually closer to the relegation zone by four points.
Alternatively, the former Barcelona forward may just have chose to go out on a high, potentially helping Arsenal win a trophy or qualify for the Champions League before he leaves.