The Spain international did not travel to Germany with the rest of the squad due to a hamstring injury. The game against Dortmund is of little significance to City, as they are already eliminated from the Champions League.
But Mancini made it clear that Silva was not being rested as a precaution, explaining that he is unsure as to whether the 26-year-old will be fit for Sunday's clash with Manchester United at the Etihad.
"[David] Silva is not here because he has a hamstring injury, and we do not know at the moment if he can recover in time for the derby," the Italian told reporters.
"We will try, but we will have to see."
The match is a must-win for the champions, who currently sit three points adrift of United at the top of the Premier League.
It's a further blow for Mancini, with James Milner (hamstring), Aleksandar Kolarov (groin) and Gael Clichy (foot) all doubtful for the tie.