"I have left Pastore to rest because he has been less good for a few weeks. He needs to recuperate with a specific programme," Kombouare was quoted as telling a news conference in Salzburg by the club's website.
"But it is not a sanction at all."
PSG, who spent more than 80 million euros on the transfer market in the off-season, have been struggling lately after a bright start to the season.
They have lost their last two Ligue 1 games, 1-0 at home against Nancy and 3-0 at bitter rivals Olympique Marseille on Sunday, with Pastore, who joined from Palermo on a French record 42-million-euro transfer in August, appearing a shadow of his usual, brilliant self.
PSG have dropped to second in Ligue 1, three points behind surprise package Montpellier, and lie second in their Europa League Group F three points adrift of Athletic Bilbao.
A defeat on Thursday could cost Kombouare his job, with media reports suggesting that former France midfielder Claude Makelele, now an advisor to general manager Leonardo, could take over on a caretaking basis.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.