The move will anger the Chief Rabbi and senior clerics such as the former Archbishop of Canterbury, Lord Carey, who has argued that Israel needs the support of the Church.
But speakers in the debate argued passionately that the Church must be seen to be investing its money for the common good, and not merely for the best financial return.
Keith Malcouronne, from Guildford, said he had received a letter of support for disinvestment from the Anglican Bishop of Jerusalem, the Rt Rev Riah Hanna Abu El-Assal.
The Bishop of Chelmsford, the Rt Rev John Gladwin, said Christians in Palestine were in despair, and he held the Israeli government to blame.
Caterpillar may be a company being used for dreadful purposes across the world, but the problem is not Caterpillar. The problem is the situation in the Middle East and the government of Israel," he said.
The Rev Simon Butler, from Southwark, south London, warned Caterpillar that "in our understanding of sin, acts have consequences".
But the Bishop of St Albans, the Rt Rev Christopher Herbert, who is chairman of the Council of Christians and Jews, suggested that the debate was unbalanced.
He said there was a "belief and hope" in the Jewish community that Christians would understand their perspective in such debates, but the Synod had not reflected the complexity of the situation.
The vote will rekindle the row that followed the decision last summer of the Anglican Consultative Council, representing the worldwide Church, to back a report urging it to disinvest in companies that "support the occupation".
Lord Carey said at the time that approval of the report would be "disastrous" for peace efforts in the region.
He said the Israelis already felt traumatised by attacks on them and this would be "another knife in the back".
The Chief Rabbi's office and the Board of Deputies also made strong private representations to Dr Williams.
A spokesman for the Chief Rabbi said last summer that a policy of disinvestment "would not only be misguided, particularly at the present time, but it would have worrying effects on the long-established ties between Jewish and Anglican communities worldwide".