Son scored a sublime individual goal - his 50th for the club - as Spurs put on a scintillating display to end their London rivals' unbeaten start to the Premier League season with a 3-1 win at Wembley.
Dele Alli and Harry Kane also found the net, but Chelsea's defence were unable to cope with Son's speed.
His goal, where he outpaced Jorginho and then made a mug of David Luiz before slotting home, was the crowning moment of the South Korean's season, which has been disjointed to say the least.
Having been at the World Cup with South Korea in the summer, he returned to international duty with his country in August in a bid to earn exemption from military service by winning the Asian Games - a feat he achieved.
But that gruelling schedule took its toll on the 26-year-old and he had been a shadow of his usual self in the wake of those international exertions.
Spurs' reward for allowing Son to go to the Asian Games was the promise he would not be called up for the most recent international break and Pochettino reckons that was a good bit of business.
"You can see on the pitch, Son's performance was fantastic and you can see he deserved it because the summer for him was very difficult," the Argentinian said.
"In the last international break he was here, training hard. It is one of the reasons that he showed he is fresh, his physical condition is much better and I think it is going to help him for the rest of the season."
Son could have already had four goals by the time he finally beat Chelsea goalkeeper Kepa Arrizabalaga.
Pochettino said of his goal: "It was fantastic, everyone that saw the game was in love with the action.
"It was fantastic action, talent. It was a fantastic capacity to make what he made, it was an outstanding action for a very good player like him."
Chelsea had gone without a defeat in their opening 12 Premier League games and it was their first loss in any competition under Maurizio Sarri since the Community Shield in August.
Sarri described his side's defending as a "disaster" and Cesar Azpilicueta admits the loss was painful to take.
"Tottenham are an aggressive team, they press well, and we were not able to get out with the ball and play our football," he told the club's official website.
"It's a tough one to take. We have to do better and it hurts to lose in this way. We have to learn from our mistakes, to improve and come back as a team.
"We need to be strong and get back to winning ways."
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