Russia is the only Security Council member to vote against the measure.
China, regarded as a Russian ally on the issue, abstained from the vote.
Western powers criticized Russia’s veto over the referendum, which will ask Crimeans if they want to rejoin Russia.
Meanwhile, Kiev has accused Russian forces of seizing a village just north of Crimea and demanded they withdraw.
Ukraine’s foreign ministry said 80 military personnel backed by four helicopter gunships and three armored vehicles had taken the village of Strilkove.
An unnamed Russian official quoted by Pravda-Ukraine said they had taken action to protect a gas distribution station from “terrorist attacks”.
Russia intervened in the Crimean peninsula after the fall of Ukraine’s pro-Moscow President Viktor Yanukovych on February 22.
The Crimean region was part of Russia until 1954 and most of its residents are ethnic Russians, many of whom would prefer to be governed by Moscow rather than Kiev.
Russia’s Black Sea fleet is also still housed in Crimea.
But Russia has signed agreements promising to uphold Ukraine’s territorial integrity.
Crimea’s regional parliament instigated the secession referendum after lawmakers voted overwhelmingly to support rejoining Russia.
However, the national parliament in Kiev ruled the referendum unconstitutional, and earlier on Saturday voted to disband the regional assembly.
At the UN, 13 members of the Security Council backed a resolution that called for all nations to respect Ukraine’s territorial integrity and condemned the referendum as illegal.
Western diplomats had expected Russia to veto the document, but got what they wanted when China abstained.
China and Russia usually work in tandem at the Security Council.
But Beijing is sensitive about issues of territorial integrity, because of fears it could send a message to its own restive regions of Tibet and Xinjiang.
America’s UN envoy Samantha Power said it was a “sad and remarkable moment” and labeled Russia “isolated, alone and wrong”.
Samantha Power said Sunday’s referendum was “illegal, unjustified and divisive” and would have no effect on the legal status of Crimea.
Russian envoy Vitaly Churkin said the referendum was necessary to fill the “legal vacuum” since Ukraine’s “coup d’etat” last month.
Earlier in Moscow, tens of thousands rallied against Russia’s actions in Ukraine, the biggest such protest in two years.
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