The draft resolution, drawn up by the United States, urged nations not to recognize the results of the vote, widely expected to back Crimea, a southern Ukrainian region with a narrow ethnic Russian majority, joining Russia.
Russian UN Ambassador Vitaly Churkin said Moscow will respect the choice of people in the region that has refused to recognize the legitimacy of the new central government in Kiev.
China, a close ally of Russia, abstained from the vote.
"This initiative had no grounds: events in Ukraine pose no threat to the international peace and security, the issues that the Security Council deals with under the UN Charter,” Churkin said.
Churkin criticized the UN member-states for their biased approach on the deepening crisis in Ukraine and said the draft resolution was apparently aimed at politicizing situation in Crimea.
Authorities in Kiev and international leaders have condemned the referendum as illegitimate and threatened Moscow with sanctions over its apparent plan to annex the region.
Crimea is one of several Ukrainian regions that have rejected as illegitimate the government in Kiev that ousted President Viktor Yanukovych on February 22 after months of street protests following his step back from closer ties with the European Union.