Harry Kane, who has been on fire for Spurs in recent months, clocked his 18th goal of the season in the 49th minute after a scoreless first half.
But Palace responded well and when Benjamin Stambouli felled Joe Ledley in the box they were level as Dwight Gayle scored from a penalty kick. Jason Puncheon completed the win in the 80th minute with the ground buzzing with excitement as the side dominated a recently successful Tottenham.
Pochettino believes that the penalty was the game changer with the manager insisting it wasn't a clear-cut decision.
"Yes [decisions were key today]," he said, according to BBC Sport. "After I think 65 minutes we were in control of the game, the penalty changed it all, the energy, it changed all.
"The decision, maybe it wasn't a penalty and it is key in the result. From my dugout it's difficult to give my opinion but my players say he never touched the player."
Kane had a similar penalty shout during the match and while Pochettino wouldn't dwell on it he did feel Tottenham may have been slightly aggrieved over the course of the game.
"Harry Kane's [penalty shout] was the same as the penalty for Crystal Palace," he explained. "Difficult to see from my position, but one against us and though we conceded another goal, maybe it's important, this decision.
"It was difficult after we conceded the goal. They showed more energy than us in the last 15 or 20 minutes. For that I'm disappointed, after we conceded, Crystal Palace were better."
Tottenham could have moved into the top four with a win but they now stay in fifth position in the table, two points behind fourth-placed Southampton who play Manchester United this weekend.