Sergio Aguero - hailed as the best striker in the world by Pochettino earlier this week - scored all of City's goals in an eventful match at the Etihad Stadium that saw referee Jon Moss award four penalties, three of those to the hosts.
Tottenham's Federico Fazio was sent off on his full Premier League debut for the foul that resulted in City's third penalty - and a second successful conversion from Aguero.
While Pochettino conceded Fazio's dismissal all but ended the game as a contest, as Manuel Pellegrini's men moved 3-1 up with 22 minutes to play, the Tottenham manager also reflected on the impact of two earlier incidents.
City's first spot-kick came after Erik Lamela had been penalised for a foul on Frank Lampard, while Joe Hart made a fine save to deny Roberto Soldado with the score at 2-1, moments after keeping out a penalty from the Spurs striker.
"The first key moment was the first penalty, because for me it wasn't a penalty," said Pochettino.
"And after our penalty, the second chance ... a big save [from] Joe Hart - this was the [second] key moment."
Tottenham have now shipped 15 goals in their last three Premier League meetings with City, having lost 6-0 and 5-1 to Pellegrini's side last season.
Pochettino was not too downbeat, however, and defended his decision to select Fazio alongside captain Younes Kaboul in the heart of defence, pointing to the pair's freshness due to their lack of action in the international break.
"I'm disappointed with the result, because it's tough to us, but I think we need to take positives from this game and improve," he added.
"I think Fazio was good. He had a good performance. It's a shame, the penalty and the red card."
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