Jury chairman Zhang Yimou said the judges had reached the decision quickly and unanimously - "a first in my experience with film juries," he added.
Negishi also took the Best Director award, while star Koichi Sato scooped the Best Actor prize.
To further ice the cake, the film won the Audience Award.
Set in Hokkaido, Japan's northernmost main island, in mid-winter What the Snow Brings depicts the struggles of a failed businessman (Yusuke Iseya) to get his life back on track, while working as a stableboy for his gruff older brother (Sato), a trainer who prepares draft horses for sleigh-pulling races unique to the island.
It was produced by indie outfit BeWILD and is being distributed in Japan by Bitters End.
Best Actress prizes were given to Helena Bonham Carter, for her work in Hans Canosa's Conversations with Other Women, and to 84-year-old first-time screen performer Jin Ya-quin, for playing a lonely elderly woman in Ma Liwen's You and Me. Conversations with Other Women also won the Special Jury Prize.
The Award for Best Artistic Contribution went to another Chinese film, Yang Ya-zhou's Loach Is Fish Too.
In the 11-film Japanese Eyes section for new Japanese films, started last year, Mitsuo Yanagimachi's drama Who's Camus Anyway took the Best Picture Award. The Special Award went Masaki Kobayashi's mockumentary Ski Jumping Pairs - Road to Torino.
In the Winds of Asia section Yasmin Ahmad's Sepet (Slit Eyes) won the Best Asian Film Award, while Eric Khoo's Be With Me took the Special Mention prize.