On 13 April 1986, Toaff was greeted by, and prayed with, Pope John Paul II during a visit to the Great Synagogue of Rome, the first by a reigning pope to a Jewish house of worship. Rather than extending his hand for a formal handshake, Toaff embraced the Pope. On April 7, 1994, Toaff co-officiated at the Papal Concert to Commemorate the Shoah at the Sala Nervi in Vatican City, along with Pope John Paul II, and the President of Italy Oscar Luigi Scalfaro.