Patriarch of Moscow and All Russia Alexy II said in his letter: "With absolute respect for your country's laws, I beg you to show mercy to the man who accepted Christianity 16 years ago."
The Patriarchate said the spiritual leader called for tolerance, spoke against forceful measures in religion.
Abdul Rahman, 41, was imprisoned earlier this month for converting to Christianity. Under Islamic Sharia law, an apostate from Islam can face execution.
After pressure by Western countries, which had helped the incumbent authorities to power, Rahman was released Tuesday and allowed to leave Afghanistan. A special session of the parliament's lower house condemned his release as contrary to Islamic laws.
Rahman became a Christian while working with an aid group to help Afghan refugees in Pakistan 16 years ago. He then moved to Germany. On returning to Afghanistan, he was arrested following a dispute between his relatives, who announced his apostasy.
