Referee Anthony Taylor showed Gusto a yellow card for his foul on former Chelsea winger Willian in the 38th minute, even though the France defender carried through after winning the ball and landed his boot on the Brazilian's ankle.
"In the Premier League, in 10 moments like that one, nine have been a red card," Silva told reporters.
The Portuguese coach said he thought it was a clear mistake by the VAR team not to advise Taylor to reconsider his decision.
Chelsea won the derby 1-0 after Cole Palmer coolly converted a penalty in the dying minutes of the first half after Fulham’s Issa Diop had brought down Chelsea’s Raheem Sterling.
Pochettino acknowledged Silva’s frustration about the decision.
"Of course, if I am put in his place I am going to tell you it’s a red card," the Argentine told reporters.
He said a similar decision went against Gusto this season when he was shown a red card for a foul on Aston Villa's Lucas Digne.
"I remember the game against Aston Villa, it was a red card and I didn't complain about that, but today it was a yellow card," Pochettino said.
The Chelsea coach said he was happy with his team's performance - their third league win in a row - although he continued to lament their inability to turn long periods of dominance into goals.
"We should have scored another goal or two and killed the game," Pochettino said.
