Andrea Pereira gave the Cottagers a lead within less than one minute after Bukayo Saka’s mistake before the England international levelled from the spot after the break.
Eddie Nketiah looked to have completed a turnaround for the Gunners three minutes later when latching onto Fabio Vieira’s cross but Joao Palhinha struck late to earn Silva’s side a point.
Calvin Bassey was sent off for two yellow cards on his full debut for the club, the first coming as a result of time wasting before the second was shown after the defender had hauled down Nketiah.
Speaking after the game, Silva said: “The first yellow card for Calvin is a joke.
“I have to say that yellow card is a joke. Of course we understand the new circumstances, they [the new rules] are taking all the emotion from the game.
“It’s just going to protect the big clubs because you have to see consistency in the big decisions.
“For sure, if a player from Fulham or another club came here to the Emirates and takes ten seconds to throw the ball in from a throw-in or a goal kick, it will be a yellow card.”
Silva believes Arsenal were not given similar treatment.
“For the other clubs, it’s not the same.
“If you see one of the first throw-ins for [Thomas] Partey on my side of the touchline, it took much more time than Calvin with the goal kick.
“It was not a yellow card. Why? Because they were losing the game.”