In an interview ahead of the gala ceremony he spoke of being honoured to receive the Golden Bear in the country he helped to "liberate" 40 years after the Holocaust with his iconic nine-and-a-half-hour work.
"During the 12 years of work on 'Shoah' I had enormous difficulties that almost led me to abandon it, but one of the things that kept me going was that I thought 'Shoah' would be a film to help liberate the Germans," the 87-year-old said.
"I thought it would help Germans to confront their horrible past. Do not forget that they remained silent for many, many years. The immensity of the crime silenced them, they couldn't even talk about their own suffering."
The film, which includes harrowing interviews with Holocaust survivors and footage taken at several Nazi death camps, had its German premiere at the Berlin festival.
"I remember that there were three or four screenings of the entire film. The cinemas were packed and peoples' knees were shaking. It was very hard for them to see the film and it was very hard for me to show them," he said.
"Occasionally someone would get up, I thought, 'He's leaving, he can't stand it anymore.' But he went out, had two drags on his cigarette and returned."
Lanzmann said the screenings were followed by all-night discussions with young Germans.
"It was great," he said. "In my mailbox at my hotel on the Kurfuerstendamm (then West Berlin's upscale main boulevard), there were lots of letters they wrote spontaneously, there were very nice ones among them."
Lanzmann said he was impressed by Germans' tenaciousness in facing up to their brutal history, and that he still received letters every time the documentary is shown. "'Shoah' does not have a wrinkle. The film does not age," he said.
Lanzmann said he was putting the finishing touches on a nearly four-hour-long film about Theresienstadt, a concentration camp in today's Czech Republic where nearly 150,000 people were held during the German occupation.
Festival director Dieter Kosslick hailed the director as "one of the great documentarists." "With his depictions of inhumanity and violence, of anti-Semitism and its consequences, he created a new kind of cinematic and ethical exploration. We feel honoured to honour him," Kosslick said when he announced the prize.
Lanzmann was born in Paris in 1925 to Jewish parents, fought in the French resistance against the Germans and later taught at the then newly founded Free University in Berlin after World War II.
He played a part in French intellectual life, counting amongst his circle of friends existentialist philosophers Jean-Paul Sartre and Simone de Beauvoir. Lanzmann's other films include the 1973 documentary "Israel, Why" as well as a 2001 film about an uprising in the Sobibor death camp in 1943.
"His exploration of the Shoah, anti-Semitism and political struggles for freedom infuse both his cinematic and journalistic work," said the Berlinale.