Ivory Coast international Aurier is sidelined with a recurring ankle injury, coach Unai Emery said on Monday ahead of the Group A game at St Jakob Park.
"He has been having problems for a few months. He's been playing through pain and we have decided to let him fully recover," Spaniard Emery told a news conference.
Belgium international Thomas Meunier, who deputised last Friday in a 1-0 Ligue 1 win at Lille, is expected to start against Basel.
Argentina midfielder Pastore has been sidelined for a month with a calf injury and is now back in the squad.
"He's coming back gradually so we will see if he takes part in the game," Emery said.
PSG, who beat Basel 3-0 in Paris earlier this month, are second in Group A with seven points from three games, behind Arsenal on goal difference.
Basel and Ludogorets have one point.