Defender Kimpembe went off after 18 minutes after suffering an injury to his left hamstring and is unlikely to return to training until early January.
Gueye lasted seven minutes longer than his team-mate and should return to training within "10 to 12 days" after also sustaining a left hamstring injury.
There is better news for Marco Verratti and Edinson Cavani, however.
Verratti has missed his side's past two games with a thigh problem but resumed full training on Monday, while Uruguay international Cavani is expected to link back up with the squad after missing the 3-1 win over Montpellier.
The club also confirmed former Manchester United midfielder Ander Herrera is set for a return to training by the end of the week after more than a month out with a thigh problem.
Thomas Tuchel's side faces Galatasaray in the Champions League before travelling to Saint-Etienne in Ligue 1.