Son, who was left distraught by the serious injury as he was consoled by team-mates and Everton players, was initially booked by referee Martin Atkinson before a VAR review deemed the challenge worthy of a red card.
"He was devastated," said Pochettino. "The players from Everton came to console him. I want to thank the captain, Coleman. He came to speak to Son. In the moment it was a little bit confusing, everyone knows on the pitch what happened, but no one believed it was intentional. When we watched on TV the outcome was very bad and we feel very sorry for Andre. The action was very bad luck.
"It was dreadful for Andre, but judge the action, not judge what happened after. We are very disappointed with this type of situation on VAR - it is there to help the referee not confuse the situation more. The referees need help. They need to go and check on the screen. In the end the decision changed everything, we were in control, we believed we were going to win the game, then we conceded the goal.
"The VAR need to check if it was a bad tackle and not a bad injury. It was clear that it was never the intention of Son to create the problem that happens after. It was unbelievable he received the red card. I never complain about the VAR, but please - we need use it in the best way. It is going to change the spirit of football."
Pochettino added: "I was the first or only coach in the Premier League that was against the VAR.
"This type of situation, that you need to help because the decision of the referee was yellow card. It is creating a big, big mess. For me, I love that the referees are the boss on the pitch.
"We feel very disappointed. Then, everything changed. I think it was under control for Tottenham. Then we concede a goal playing with one less. It is very difficult to understand this type of situation happened."