The gesture of respect took place at the site where several German officers were executed following their attempt to assassinate Adolf Hitler in 1944.
"It was a very moving moment," actor Christian Berkel told the German newspaper Bild am Sonntag.
Berkel said Cruise, director Bryan Singer and screenwriter Christopher McQuarrie said a few words and requested the silence "out of respect for the place and out of respect for the life achievement of these people who were executed there," the BBC said.
The German government initially banned the filmmakers from shooting "Valkyrie" on the site, which is a memorial to the Third Reich resistance fighters, because of experiences with other film productions and because it wanted to preserve the dignity of the site.
However, the decision was reversed and filming began last week at the Bendler Block after the filmmakers convinced officials they would treat the spot and those who died there with the regard they deserved.