The draft resolution, which says Sunday's referendum would have no validity, got 13 votes in the 15-member council. But it was rejected when permanent member Russia exercised its veto.
"Russia, isolated, alone and wrong, blocked the resolution's passage," US ambassador Samantha Power told the council at its seventh emergency session on Ukraine since the crisis began.
"This is a sad and remarkable moment," she said.
"As we speak, Russian armed forces are massing across Ukraine's eastern border," she added in a short speech.
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Chinese ambassador Liu Jieyi said that passing a resolution on Ukraine at this moment would "only result in confrontation and further complicate the situation."
"China has always been fair and objective. We will continue to mediate and promote dialogue so as to play a constructive role in seeking a political solution to the crisis," he said.
He called for an international coordination mechanism to explore as soon as possible a political settlement, all parties to refrain from escalation, and for international financial institutions to help shore up economic stability in Ukraine.
Beijing has long defended the need to respect territorial integrity and does not back interference in the internal affairs of other countries.