Waves of violence and vandalism targeting Jews have hit Europe in the past few years. Last week, worshippers in a Moscow synagogue were attacked by a man with a knife.
Benedict did not mention specific occurrences of anti-Semitism in his speech to greet Rabbi Riccardo Di Segni in an audience at the Vatican.
The rabbi led a delegation from Rome's Jewish community, one of the oldest in the world.
The German-born pontiff said Jews and Christians have the responsibility to cooperate to promote justice, love and freedom.
"In the light of this common mission, we cannot not denounce and combat with decisiveness the hate and incomprehension, the injustices and the violence that continue to sow worry in the soul of men and women of good will," Benedict said.
"In this context, how can one not be pained and worried about the fresh outbreaks of anti-Semitism that are occurring?" the pope said.
Di Segni invited Benedict to visit Rome's main synagogue, noting the approaching 20th anniversary of Pope John Paul II's groundbreaking visit there, which helped repair centuries of poor Vatican-Jewish relations.
Benedict became the second pope in history to visit a Jewish house of worship - after John Paul - when he visited to the synagogue in Cologne, Germany, last summer during his first trip abroad since being elected pontiff in April.
The Cologne synagogue visit appeared to help smooth over Israeli-Vatican tensions sparked by Benedict's failure to mention attacks on Israelis during a condemnation of terrorism.
Di Segni thanked Benedict for "denouncing anti-Semitism, past and present, for condemning fundamentalist terrorism, for his attention to the state of Israel, which, for all the Jewish people is an essential and central reference."
The rabbi said he was convinced that under Benedict, the Catholic Church's commitment to better relations with Jews would continue.
Benedict said he felt "great joy" over the rabbi's visit.
"The people of Israel have been liberated several times from the hands of enemies, and in the centuries of anti-Semitism, in the dramatic moments of the Shoah, the hand of the Almighty has sustained and guided it," the pope said, using the Hebrew term for the Holocaust.
Church officials in Poland have invited Benedict to visit Auschwitz during a Polish tripn he is expected to make this spring. The exact dates and itinerary of the pilgrimage have not yet been announced.
Jews widely admired John Paul for his unstinting efforts to promote Jewish-Catholic reconciliation, including his 1986 synagogue visit in Cologne and his 2000 visit to Israel. John Paul also won many Israeli hearts by apologizing for Roman Catholic wrongdoing over the centuries.