He was welcomed by President Ezer Weizman, Prime Minister Ehud Barak and a host of Israeli political and religious dignitaries who lined up under rainy sky to greet him.
Israel is the second stage of a week-long spiritual journey which will take the Pope to the most sacred Christian sites in the Holy Land.
Click for sacred sites on the Pope's tour
This is only the second time a Pope has visited Israel - and Pope Paul VI's trip in 1964 did not have official status.
A Royal Jordanian Airlines plane carrying the Pope and his entourage landed at Tel Aviv airport after a brief flight from the Jordanian capital, Amman.
'Welcome to the Holy Land'
"Welcome to the Holy Land," said Prime Minister Ehud Barak as he shook the pontiff's hand, after John Paul II touched his lips to a bowl of Israeli soil carried by three children - a Christian, a Muslim and a Jew.
In a welcoming speech, Israeli President Ezer Weizman paid tribute to the Pope's struggle against anti-Semitism.
"We appreciate your role in condemning anti-Semitism as a sin against heaven and humanity and we appreciate that you have also asked for a pardon for the crimes committed against the Jewish
people in the name of the Catholic church," he said.
Soon after arriving, the Pope went by helicopter to Jerusalem.
The Vatican, which only recognised the state of Israel in 1994, does not recognise its claims over east Jerusalem, which the Jewish state captured and annexed in 1967.
Telegram
During his flight from Amman to Tel-Aviv, the Pope sent a telegram to Palestinian leader Yasser Arafat.
In his message, John Paul II said: "In eager anticipation of my visit to Bethlehem and the Palestinian territories I ask Almighty God to bless the Palestinian people and to strengthen in all the peoples of the Middle East the resolve to bring about a just and stable peace in the region."
The Pope's pilgrimage around Israel and the Palestinian territories will culminate in final prayers at the site in Jerusalem where Christians believe Jesus was resurrected from the dead.
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