The resolution, which also condemned Israel's "outrageous attack," was adopted after a vote, with 32 countries voting in favour, three against, and eight abstentions.
It "decides to dispatch an independent international fact-finding mission to investigate violations of international law, including international humanitarian aid and human rights law, resulting from the Israeli attacks on the flotilla of ships carrying humanitarian assistance."
The text also decides to "authorize the president of the council to appoint members of this independent international fact finding system."
Meanwhile, the United States declined to condemn Israel for its raid on a humanitarian flotilla headed for Gaza, but said the incident showed Middle East peace talks were needed "more than ever".
The White House and US Secretary of State Hillary Clinton did describe the situation in Gaza as "untenable" and "unacceptable," but Washington's reaction on Tuesday to the raid did not match the explicit rebukes of Israel of some of its allies.
As diplomatic fallout multiplied, and threatened to derail a laborious bid to broker Israeli-Palestinian peace talks, US President Barack Obama also called key regional power broker, Turkish Prime Minister Recep Tayyip Erdogan.
Obama spokesman Robert Gibbs was earlier asked directly whether his boss would condemn Israel over the drama in international waters in which, he said, at least 10 people were killed by Israeli commandos.
Speaking carefully, Mr Gibbs stuck to the language of a UN Security Council statement issued late Sunday on the raid.
The statement condemned "those acts which resulted in the loss of at least 10 civilians and many wounded", but did not specifically say whether the Israeli raid or actions of pro-Palestinian supporters caused the violence.
It also called for a "prompt, impartial, credible and transparent" inquiry into the incident conforming to international standards, he noted.
"We're obviously supportive of that."
Mrs Clinton said Washington supported an "Israeli investigation that meets those criteria. We are open to different ways of assuring a credible investigation, including international participation."
State Department spokesman Philip Crowley explained why Washington thought Israel should carry out the investigation rather than an independent international body.
"These were Israeli forces that carried out this action and we think they're in the best position to investigate what instructions were given to these forces, how was the situation when they approached the flotilla, and what transpired on board that ship."
Mrs Clinton also criticised the humanitarian situation in Hamas-ruled Gaza under an Israeli blockade, calling it "unsustainable and unacceptable" while Mr Gibbs said the incident showed a Middle East peace plan was needed "more than ever".
The deadly maritime confrontation threatens to stymie US peace moves again at a time when the Obama administration has just restarted "proximity" peace talks between Israel and the Palestinians.
But Mr Gibbs said that he did not think the incident, which triggered global fury, would have "a great impact" on Washington's ties with the Muslim world, despite staunch US support for Israel.
Israel has blamed activists on a Turkish vessel, Mavi Marmara, for the confrontation, saying its troops were attacked as they boarded the ship and that nine passengers were killed in the ensuing fight.
But passengers disputed that version of events, saying that those on board were not armed with anything more threatening than a few wooden batons. A greek activist who was released by Israel said Israeli troops used bullets, gas and electroshock weapons to subdue those on board the aid flotilla.
The showdown provoked a crisis in Israel's relations with Turkey - once its closest Muslim ally - as diplomatic sources in Ankara confirmed at least four of the dead were Turkish.
It also provoked another diplomatic headache for Washington, as Mr Obama had expended considerable effort trying to maintain good relations with Turkey, a rising regional power which is also key in the confrontation with Iran.
In his call with Mr Erdogan, who earlier branded the raid a "bloody massacre" Mr Obama expressed his "deep condolences for the loss of life and injuries resulting from the Israeli military operation against the Turkish-flagged ship bound for Gaza", the White House said.
"The President affirmed the importance of finding better ways to provide humanitarian assistance to the people of Gaza without undermining Israel's security."
Israeli Prime Minister Benjamin Netanyahu had been due at the White House on Tuesday for talks seen as an effort to move on from recent and rare public disagreements with the US.
But he cancelled the visit to return home to deal with the crisis. The White House said that Mr Obama's talks with Palestinian leader Mahmoud Abbas next week were still on as scheduled.
In a sign of domestic political pressure on Mr Obama over Israel, a top Republican lawmaker Eric Cantor called on him to veto any "biased UN resolutions reining in Israel's right to defend itself".
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