"Benzema is injured. Karim has a thigh muscle problem. He is out. I don't know how long for, but he is out for tomorrow," Mourinho told a news conference on Monday.
The German champions triumphed 2-1 against Real on home turf two weeks ago to take the top spot in Group D with seven points, one ahead of the nine-time European Cup winners who are second.
Real have reacted well to the reverse, rattling in 13 goals in the three games since then but they will be without Mourinho's favoured leader of the line at the Bernabeu.
Argentina striker Gonzalo Higuain, who has netted seven in the league but none in Europe so far, is the obvious replacement.
Real are one of the favourites to win the competition and hold a three-point lead over third-placed Ajax.
Big-spending Manchester City are bottom with only one point, though Real still have to visit the Etihad stadium later this month.
"It is a tough group and any point you get is good," said Mourinho, who called some of the Champions League groups a "joke" after the 2-1 loss at Dortmund.
"Dortmund and ourselves are the best situated, but it is possible that City collect more points in the second round of matches and come back. All the teams are under pressure," added the Portuguese.
Mourinho's side have won seven home matches on the trot in Europe and last lost in front of their own fans in a King's Cup quarter-final clash against Barcelona 10 months ago.
Filling their own stadium, however, appears to be a problem despite the importance of Tuesday's game, with a large number of tickets reportedly unsold.
"It's one of the few things that hasn't been pinned on me yet," Mourinho said when asked about ticket sales.
"I don't think I am responsible for the economic crisis in Spain and in Europe."