Egyptian doctor Mohammed Helmy will be presented posthumously with the "Righteous Among the Nations" medal and certificate at a ceremony on Thursday in Berlin.
Helmy's great-nephew is to accept the honour.
Helmy had already been recognized back in 2013 as a "Righteous Among the Nations" - the first Arab to be recognized as such - but the Yad Vashem Holocaust memorial said it had not been able to contact the doctor's next of kin.
Members of Helmy's family reportedly did not want to accept the honour because of its link to Israel, reports which were never confirmed by Yad Vashem.
However, the efforts of an Israeli filmmaker seemed to have helped reach a resolution.
Filmmaker Taliya Finkel was inspired by the story of an Egyptian saving Jews in Nazi Berlin and set out to make a movie about it, she said.
Her work led her to Helmy's great-nephew, Dr Nasser Kotby, also a physician, who will be travelling from Egypt to receive the honour in his great-uncle's name.
Helmy had hidden a young Jewish woman, Anna Boros, in a property he owned during the war, while also finding places for her grandmother and giving medical care to her parents.
'Something about him'
Finkel's film, which includes animation of the historic events and is called "Anna and the Egyptian Doctor," brings together relatives of Boros and Helmy and accompanies them to the sites of the families' story.
She contacted Boros's daughter, US-born Carla Gutman Greenspan, and through a German producer, Finkel reached Helmy's family in Egypt.
Helmy had died childless in Berlin in 1982.
Finkel contacted Kotby and told AFP she had "built a relationship based on trust and friendship".
Relations between Israel and Egypt, which are bound by a peace treaty since 1979, remain strained by Israel's policies toward the Palestinians.
Kotby was nonetheless willing to participate in the film.
"He admires Helmy, who was like a father to him," Finkel said of Kotby. "I told him this was the way to eternalize the story."
Kotby receiving the Righteous Among the Nations award was Finkel's idea for her film's finale. "I said, 'let's wrap up the film nicely,'" she said.
The award is to be handed to Kotby at the German foreign ministry by Israel's ambassador to Germany, Jeremy Issacharoff.
Irena Steinfeldt, director of the Righteous Among the Nations department at Yad Vashem, said that Helmy, who himself was targeted by the Nazis, "saw the persecuted as human beings, and felt it was his duty to stand up and act."
"Helmy's humanity shows that every person, however marginalized by society, can make a difference," Steinfeldt said.
Finkel said she felt a personal connection to Helmy.
"There's something about him," she said. "He realized he couldn't change the world but that he could save the girl."
Yad Vashem says it has recognized more than 26,500 Righteous Among the Nations, including around 70 Muslims.