A Church of England decision to review its investments in firms whose products are used by Israel in the occupied territories has been criticised.
Sir Jonathan said the vote would harm Jewish-Christian relations
Britain's most senior Jewish leader said the Synod's vote was "ill-judged" and would "hurt Israel without helping the Palestinians".
Chief Rabbi Sir Jonathan Sacks told the Jewish Chronicle the move could damage Jewish-Christian relations in the UK.
The Church said the decision was only advice to its ethical advisory group.
In his article, Sir Jonathan said: "For years, I have called on religious groups in Britain to send a message of friendship and co-existence to conflict zones throughout the world, instead of importing those conflicts into Britain itself."
The effect of the Synod vote would be the opposite, he added.
"The Church has chosen to take a stand on the politics of the Middle East over which it has no influence, knowing that it will have the most adverse repercussions on a situation over which it has enormous influence, namely Jewish-Christian relations in Britain."
Sir Jonathan's remarks come after last week's vote at the Synod over whether the Church should withdraw its £2.5m investment in the company Caterpillar.
That decision followed a call from the Episcopal Church in Jerusalem and the Middle East for the Church to "disinvest from companies profiting from the illegal occupation, such as Caterpillar Inc".
The Archbishop of Canterbury Dr Rowan Williams voted in favour of reopening talks after complaints that the company's bulldozers have been used to knock down Palestinian homes.
The Archbishop has already written to the Chief Rabbi telling him that no decision about the Church's investment had been taken so far.
Looking into the issue did not "question the legitimacy of the state of Israel and its rights to self-defence", he said in the letter.
Dr Williams expressed "deep regret" at the effect on Jewish people of how the Synod's decision had been perceived and stressed that the vote did not intend or effect a disinvestment policy or a boycott.
It was rather, he said, an expression of disquiet at the prospect of the Church making financial profit from a controversial security policy.
Speaking on BBC Two's Newsnight programme the Chief Rabbi's Israel spokesman Rabbi Barry Marcus said: "There's a deep sense that the timing of this particular decision - just after Hamas has been elected, a terrorist group, and the fact that the president of Iran is calling for genocide - does make us a little uneasy."
Dean of Southwark Reverend Colin Slee said the decision was "not a case of picking on Israel".
"This is a continuing process of re-examining ethical investment and seeing whether we're behaving as we should," he told Newsnight.
The Council for Arab-British Understanding said one of the main reasons for the Synod's decision to review its investments was the Israeli policy of demolishing Palestinian homes in West Bank and Gaza Strip, which have been occupied by Israel since 1967.
Israeli soldiers have demolished 4,100 Palestinian homes since September 2000, according to Israeli human rights group B'Tselem.
A spokesman for Caterpillar said its products were sold to the US government which had then sold them on to Israel.
"We clearly have neither the legal right nor the tangible ability to regulate how customers use their machines," he added.