Helmy had moved to Berlin in 1922 to study medicine and became a urologist. He is credited with saving the life of Anna Boros Gutman and her family in 1942.
He was first nominated in 2013, but his family in Egypt refused to accept it because it came from an Israeli institution.
Prof Kotby, whose father was Helmy’s nephew, later agreed to attend the ceremony at the German Foreign Ministry on Thursday.
A Yad Vashem statement said: “Despite being targeted by the regime, Helmy spoke out against Nazi policies, and notwithstanding the great danger, risked his life by helping his Jewish friends.
“When the deportations of the Jews from Berlin began, 21-year-old Anna Boros, a family friend, was in need of a hiding place.
“Helmy brought her to a cabin he owned in the Berlin neighbourhood of Buch which became her safe haven until the end of the war. At times of increased danger when he was under police investigation, Helmy would arrange for her to hide elsewhere.”
More than 26,000 individuals from 44 countries have received the Righteous Among the Nations honour.
