The tribute was held at the site where a number of German officers were executed after an abortive attempt to assassinate Nazi leader Adolf Hitler in 1944.
Actor Christian Berkel, who stars alongside Cruise in the World War Two drama, says 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."
He adds, "It was a very moving moment."
Filming began on Friday at the Bendlerblock in Germany, after the country's Ministry of Defense overturned a ban on filming at the Berlin memorial site.
Cruise portrays Colonel Claus von Stauffenberg in the film, who was put to death after plotting to assassinate Hitler.
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