He later visited the Church of the Beatitudes on the shore of the Sea of Galilee north of the West Bank.
The Church of the Beatitudes, a Catholic Franciscan chapel, marks the spot where Jesus is believed to have preached his Sermon on the Mount, laying out core teachings and his call to "turn the other cheek".
Bush also visited the ruins of the ancient village of Capernaum where Christians believe Jesus performed miracles.
The US president said he hoped to return to Israel for its 60th independence celebrations in May.
Bush has had individual talks with Mahmoud Abbas, the Palestinian president, and Olmert, during his three day trip, telling them: "Now is the time to make difficult choices."
In what is being called a hardening of his tone, Bush on Thursday urged an end to the occupation of the West Bank and pushed for a peace treaty to be signed within a year to create a Palestinian state.
Speaking to reporters in Jerusalem after returning from the West Bank, he said: "The establishment of the state of Palestine is long overdue. The Palestinian people deserve it.
"There should be an end to the occupation that began in 1967."
Bush pressed the Palestinians to rein in armed groups.
He said any negotiations must also ensure Israel has "secure, recognised and defensible borders" alongside a "viable, contiguous, sovereign and independent" Palestine.
The US president also shocked Palestinians while in Ramallah, saying they needed to move past previous UN resolutions that "did not work", such as those calling for the dismantling of Israeli settlements and a right of return for Palestinian refugees.
Bush reiterated in the keynote statement a vision of territorial compromise he first charted in a policy letter to Ariel Sharon, the Israeli prime minister in 2004, advocating mutually agreed changes in armistice lines set in 1949 after fighting with Arab armies that accompanied Israel's foundation.
Bush said he had urged Abbas and Olmert, whom he met on Wednesday and again on Thursday, "to make sure their teams negotiate seriously, starting right now".
It was Bush's first visit to Israel and the West Bank in seven years as president. His administration said he is likely to return before the end of his tenure.
He has asked the Arab nations to assist Abbas in peace efforts and curb Iran's influence in the region.
Bush's visit to the region coincided with increased violence among Israelis and Palestinians.
According to the Palestinian Centre for Human Rights, 99 Palestinians have been killed in violence since Israelis and Palestnians sat down together for peace talks in the US city of Annapolis in November.