Dr. Helmy, who died in 1982, was represented by his great-nephew Nasser Kotby who received the award on his behalf at the Israeli embassy in Berlin.
Mohamed Helmy was working at a hospital and studying medicine in Berlin before World War Two. He himself faced racial persecution, losing his job and twice being arrested by the Nazis.
Dr. Helmy hid one of his patients, 21-year-old Anna Boros, from Gestapo at a hiding place at his property until the end of the war in 1945. He also assisted Boros' stepfather, mother and grandmother.
"Dr. Helmy did everything for me out of the generosity of his heart, and I will be grateful to him for all eternity," Boros later wrote.
Dr. Helmy was recognized as Righteous Among the Nations by Israel's national Holocaust Memorial institution, Yad Vashem, in 2013.
Some 70 Muslims are recognized by Israel as saviors, but Dr. Helmy is the first Arab.