"I find it moving to recall that Jesus, as a young boy, heard the words of Scripture and prayed in a place such as this," he said.
At a Roman Catholic church in Manhattan, the pope later warned other Christian leaders against "so-called prophetic actions" that conflict with traditional views of the Bible, a reference to the debate over Scripture that is fracturing churches in America and around the world.
In his visit to the synagogue, Benedict was shown the congregation's collection of parchment scrolls, and two youngsters presented him with the Passover gifts.
The German-born pontiff then offered a gift of his own: a reproduction of a Jewish codex.
"In our lifetime, we have experienced the ravages of war, the Holocaust, man's inhumanity to man and tasted the joy of freedom," said Rabbi Arthur Schneier, who lived in Nazi-occupied Eastern Europe.
"This momentous occasion takes places on American soil, where men and women escaping the clutches of oppression and religious persecution have built a nation of democracy and freedom. This is a nation which has allowed all religious communities to flourish."
The Jewish community makes "a valuable contribution to the life of the city," Benedict said. "And I encourage all of you to continue building bridges of friendship with all the many different ethnic and religious groups present in your neighborhood."
The visit was Benedict's second as pontiff to a Jewish house of worship. On his first papal trip abroad in 2005, Benedict entered a synagogue in Cologne, Germany, that had been destroyed by the Nazis and rebuilt.
At his visit with Christian leaders, the pontiff said allowing individual congregations to interpret the Gospel undermines evangelism at a time when "the world is losing its bearings" and needs "persuasive common witness" to salvation in Christ.
"Only by holding fast to sound teaching will we be able to respond to the challenges that confront us in an evolving world," Benedict said at the evening service with Protestant and Orthodox clergy at St. Joseph's church, which was founded by German immigrants and still regularly celebrates Mass in German.