Prince Charles brought flowers from his garden at Birkhall to lay at Princess Alice of Greece's grave in the Church of St Mary Magdalene, above the Garden on the Mount of Olives.
Heir to the throne Charles paid his respects at the crypt of the Duke of Edinburgh's mother, after attending former Israeli president Shimon Peres' funeral on Friday.
She died in 1969 and her remains lay at first in St George's Chapel, Windsor. But her final wish was to be buried at the Russian orthodox convent on the Mount of Olives, near her aunt Elizabeth, the Grand Duchess of Russia, who was murdered by the Bolsheviks and declared a Russian Orthodox saint.
Charles also placed flowers at the grave of his ancestor the Grand Duchess.
The Prince was accompanied by the head of the Russian Ecclesiastical Mission in Jerusalem, the Very Rev Archimandrite Roman Krassovsky.
Alice was re-interred in Jerusalem in 1988, but it was not until 1994 that the Duke of Edinburgh visited his mother's grave when he travelled to Israel for a ceremony honouring her for saving Greek Jews during the Second World War.
In September 1943, the Cohen family, old acquaintances from the Greek town of Trikala, appealed to Princess Alice for refuge. She hid them in her palace until the Nazis withdrew in October 1944. During that time, the Nazis sent more than 85% of Greece's Jewish community to concentration camps.
In 1993, Alice was posthumously awarded recognition as "Righteous among the Nations" by the Holocaust Memorial, Yad Vashem.