During Tuesday's 1-1 draw, PSG's players called for handball when the ball bounced off Newcastle defender Tino Livramento's chest and against his elbow with referee Szymon Marciniak then invited to check the pitchside monitor by the VAR.
Marciniak, who had turned down a more likely penalty earlier, pointed to the spot and Kylian Mbappe scored in the eighth minute of stoppage time to secure a draw for PSG.
Kwiatkowski will be replaced by Marco Fritz.
Newcastle manager Eddie Howe slammed the decision to award the penalty, saying Livramento's hand was not in an unnatural position.