Rasoulof, 48, is currently banned from leaving Iran and was unable to accept the Golden Bear in person.
“I wish Mohammad could be here himself, but unfortunately he is not allowed to leave the country,” said producer Farzad Pak, accepting the award on his behalf.
“I would like to thank the amazing cast and crew who, put their lives in danger to be on this film.”
Rasoulof was sentenced to a year in prison last year for “attacking the security of the state”, and banned from making films for life.
He is yet to be imprisoned. His passport was confiscated in 2017 after his anti-corruption film “A Man of Integrity” premiered at Cannes.
Industry magazine “Variety” said his Golden Bear winning film was Rasoulof's “most openly critical statement yet”.
It said the film was “a series of Kafkaesque moral parables about Iran's death penalty and its perpetrators, made in open defiance of the restrictions the government put on him.”
The film tells four loosely related individual stories about the death penalty in Iran, from the executioner to the families of the victims.
“I am sorry that I will not be able to come to Berlin to watch the film alongside the audience; however, the right to choose between being present or absent at the festival is simply not mine,” said Rasoulof in a statement.
“Imposing such restrictions very clearly exposes the intolerant and despotic nature of the Iranian government.”
Picking up the award alongside Pak, fellow producer Kaveh Farnam addressed the Golden Bear directly.
“I want to ask you to hug Mohammad… my teacher, my friend, and tell him: Mohammad, you are not alone,” said Farnam.
Iranian film-makers are regularly targeted and subjected to bans, restrictions and the threat of prison sentences.