President Moshe Katsav has become the first Israeli head of state to make an official visit to the Vatican.
Pope Benedict XVI has been dubbed a "true friend of Israel"
He had a 25-minute audience with Pope Benedict XVI.
Israeli commentators say the meeting has great symbolic importance, as the two sides try to improve relations that have often been fraught.
President Katsav has invited the Pope to follow in the footsteps of his predecessor John Paul II by visiting the Jewish state.
As a gift, the Pope gave the president a copy of the Vatican document of 1965 that proclaimed that the Jews were not to blame for the death of Jesus Christ.
Mr Katsav told later told journalists that the Pope had "welcomed positively" the invitation to visit Israel, but that no date had been fixed.
"For my part, I hope it will be next year," the president said.
Security around the Vatican was extremely tight for the president's visit.
Police towed away parked cars and removed litter bins that could hide bombs.
The Israelis have called Pope Benedict XVI a "true friend of Israel".
In the first days of his pontificate he met Jewish leaders, and on his trip to Cologne he went to a synagogue.
President Katsav is on a three-day visit to Italy
But BBC Religious Affairs Correspondent Jane Little says that if the two states are to come together - as Israel hopes - to combat extremism, there is a lot of fence-mending to be done.
They recently had a diplomatic row over suicide bombings when the Pope omitted to mention an attack on Israel.
There was also the Catholic Church's eagerness to canonise the controversial wartime Pope Pius XII.
And Israel has long regarded the Vatican, which did not recognise the Jewish state until 1993, as pro-Palestinian.
For its part, the Vatican wants to resolve a stand-off over the taxation of Church property in Israel, as well as problems with visas.
Our correspondent says there is plenty of work ahead, but this meeting is a significant step towards a warmer relationship.