First-time director Adina Pintilie, 38, clutching the trophy after her surprise win, said the movie was intended to “invite you the viewer to dialogue” with its frank portrayals of sex, disability and inhibitions.
US filmmaker Wes Anderson clinched the best director Silver Bear prize for “Isle of Dogs”, an animated allegory with political bite.
Actor Bill Murray, who voices one of the pack of pooches in Anderson's first animated feature since 2009's “Fantastic Mr Fox”, picked up the award for Anderson.
“I never thought that I would go to work as a dog and come home with a bear,” he quipped.
“Ich bin ein Berliner Hund (I am a Berlin dog),” he added, riffing on John F. Kennedy's famous speech.
In a big night for female filmmakers, the runner-up Grand Jury Prize went to Polish social satire “Mug” by Malgorzata Szumowska.
The feature tells the story of a man who is shunned by his community when he has a face transplant after a horrific accident, in a plot examining tensions over identity and exclusion in eastern Europe.
“This film which is so important reflected problems not only in my own country but in whole Europe and whole world,” Szumowska said.
“I am so happy that I am a female director, yeah!” she added.
Ana Brun of Paraguay won the Silver Bear prize for best actress for her role in “The Heiresses” as a middle-aged lesbian whose partner has to go to prison for their spiralling debts.
“I'd like to dedicate this prize to the women of my country, who are fighters,” she said.
“The Heiresses”, the debut feature by Marcelo Martinessi and a rare film export from Paraguay, also scooped the Alfred Bauer Prize for opening “new perspectives” in filmmaking.
It investigates class conflict and female sexual liberation in contemporary South America in a film in which men rarely appear on screen.
France's Anthony Bajon won best actor for an emotionally raw portrayal of a young man struggling to beat his drug addiction at a Catholic Alpine retreat in Cedric Kahn's “The Prayer”.
“Museum” from Mexico, starring Gael Garcia Bernal in the true story of a daring 1985 heist by two students at the National Museum of Anthropology in Mexico City, bagged the best screenplay award.
Austria's “The Waldheim Waltz” by Ruth Beckermann about the scandal surrounding the Nazi past of former UN Secretary General Kurt Waldheim claimed the best documentary prize.
A separate Alfred Bauer Prize for work of particular innovation for costume and production design went to “Dovlatov”, a biopic about a Russian-Jewish writer grappling with Soviet state censorship in 1970s Saint Petersburg.
Last year, a tender Hungarian love story set in a slaughterhouse, “On Body and Soul”, captured the Golden Bear. It is now nominated for best foreign language film at next month's Academy Awards.