"Do you think that Sonny deserved to be booked? Unbelievable, unbelievable, unbelievable," Pochettino told reporters after the game.
"It was a penalty, the same referee," he added as he recalled an incident when the club were denied a penalty against Liverpool earlier this season.
Leicester were awarded a penalty in the second half, which Jamie Vardy missed, when midfielder James Maddison appeared to be fouled by Spurs defender Jan Verthongen.
Pochettino said Son's penalty call was an easier decision to make.
"It was so clear the position with Sonny, the action, but it wasn't clear the position of Maddison when he was on the floor," Pochettino added.
"I'm more relaxed because we won the game, three important points we got, but so disappointed with the situation because everyone wants to talk about different clubs or players.
"Do you think we are a team that is trying to cheat the referee? Come on, we are the most innocent people on the pitch."
Tottenham next play Borussia Dortmund at home in the first leg of the last 16 in the Champions League.
(Reporting by Rohith Nair in Bengaluru; editing by Sudipto Ganguly)
