Richarlison went to ground in the penalty area under a challenge from Arsenal full-back Hector Bellerin, and referee Neil Swarbrick adjudged it to be worthy of a penalty.
Hornets skipper Troy Deeney stepped up to dispatch the penalty to equalise for his side on the night, before Tom Cleverley won the game in dramatic fashion with his strike in stoppage time.
Silva said after the game: "I have seen the penalty now and I respect the decision of the referee. It's important, I didn't see a dive or a simulation.
Richarlison has suffered the most fouls in the Premier League this season, and people are starting to say he dives.
"He is not. He is fair, He wins fouls like the best players in the world win fouls."
Meanwhile Deeney, who came off the bench and was key as his side turned around the game at Vicarage Road, believes something special is happening at Watford after they continued their great start to the Premier League season under Silva.
"We have had a great start to the season and when we play the big teams we don't want to do ourselves an injustice," the Watford captain said.
"It's not a bad start, but it doesn't mean anything now.
"We are just taking it game by game. We're having a great start, we've got a great bunch, I believe we are building something really good and you can see with the late goals it shows we have got belief and that we are all in it together.
"It's a massive team effort and it's a good win and we go again on Monday."