Director Lorraine Levy's French-Israeli production took the two top honors at the prestigious festival: The Tokyo Sakura Grand Prix for best film, as well as the best director award.
The film beat 14 other productions which took part in the official competition – from Chile and the United States to Japan and South Korea.
Legendary director-producer Roger Corman, who served as chairman of the jury, said the vote for "The Other Son" was unanimous and that there were no disagreements over the decision.
'The Other Son' trailer
"Are you sure?" Levy said in her thank you speech as she received, apart from impressive and stylish statuettes, $50,000 as well. "What a beautiful day. Thank you, Tokyo."
"The Other Son," which was shot in Israel, deals with a young Tel Aviv resident (portrayed by Jules Sitruk), who enjoys writing songs and playing the guitar. The guy is about to join the Israel Defense Forces and serve in the Air Force.
Following a blood test, he discovers that his mother and father are not his biological parents, and that he is actually the son of a Palestinian family living in the West Bank, which had raised the son of the Tel Aviv family due to a mistake.
Lorraine Levy (L) with actor Jules Sitruk and producer Virginie Lacombe (Photo: AP)
"I dedicate this award from the bottom of my heart to the children of Israel and Palestine," Levy said in her excited thank you speech. Her statement was met with a round of applause.
During a press conference held after the event, the director added: "The fact that I am Jewish made me more emotionally involved in this film."
Corman added, "We chose this film as the big winner because it treats both sides in the Israeli-Palestinian conflict equally, without siding with any of them. We liked its message – that all humans are equal."