The resolution, which would also have denounced plans to build 600 new homes in Israeli settlements in the Palestinian territories, won the support of 10 of the council's 15 members.
Meanwhile, four others - Britain, Germany, Bulgaria and Cameroon - abstained.
But the "No" vote from Washington, one of the council's five permanent members with veto power, was enough to kill the resolution.
Earlier US veto
The veto follows by less than a month the US veto of an earlier Palestinian resolution, demanding Israel should back away from a threat to "remove" Palestinian President Yasir Arafat.
Palestinian UN envoy Nasir al-Qudwa said Arab states would now take the wall resolution to the UN General Assembly, where the United States has no veto and the Palestinians enjoy strong support.
While Security Council texts can carry the force of international law, assembly resolutions simply represent the will of the international community.
"We have seen tonight the second US veto in less than a month that again casts a large shadow on the possibility for the United States to exercise the role of a mediator or a broker of the Middle East peace process," al-Qudwa said.
“The apartheid wall is illegal as Israel is building it in the Palestinian territories.”
US Ambassador, John Negroponte, said the resolution would have had to denounce the main groups that had taken responsibility for human bombings in Israel, and also condemned the recent deadly attack in Haifa to avoid a veto.
"We have seen tonight the second US veto in less than a month that again casts a large shadow on the possibility for the United States to exercise the role of a mediator or a broker of the Middle East peace process"
Palestininan envoy to the UN
However, the Palestinians rejected the conditions as unacceptable.
The Security Council vote followed a six-hour public meeting at which ambassadors from dozens of nations lined up to denounce Israeli plans to prolong the barrier, already 150km long.
The US joined in the criticism of the wall plans, but argued a Security Council resolution was not the way to pursue the debate.
"US officials are engaging directly with Israeli officials on the matter of the fence," Negroponte said, adding Washington remained committed to the vision of a Palestinian state.
But al-Qudwa argued the Israeli wall plan was a land grab, aimed at colonisation rather than an "anti-terrorism" measure and would derail hopes for a Palestinian state.
He said the wall would at some point reach more than 22km into Palestinian territory, disrupting the lives of hundreds of thousands in dozens of towns and villages.
But Israeli Ambassador Dan Gillerman said the wall was meant solely to keep out "suicide" bombers and argued completing it would increase Palestinians' freedom of movement by enabling the dismantlement of roadblocks.
"Many Palestinians who oppose the fence simply want to continue killing Israelis. The Israelis building the fence simply want to live," Gillerman said.