While casting the 'no' vote, Russian Deputy Ambassador Gennady Gatilov on Wednesday accused Washington and London of rushing a resolution through the 15-nation Security Council.
The veto came three days before Saturday's referendum in Cyprus on the UN plan for reunification.
Fourteen members of the Security Council voted in favour, but Russia's 'no' vote as a permanent member was enough to block the passage of the resolution.
"In these conditions the Russian side has no other choice but to exercise a technical veto in order to ensure, in the future, conditions for normal, mutually respected work," Gatilov said.
"In these conditions the Russian side has no other choice but to exercise a technical veto in order to ensure, in the future, conditions for normal, mutually respected work"
Russian Deputy Ambassador
It was the first Russian veto since 1994.
The United Nations has been campaigning for a united Cyprus to join the European Union with nine other countries on 1 May.
But opinion polls show the UN plan faces serious opposition on the Greek Cypriot side although the Turkish Cypriot north appears to favour it.
If either side votes 'no,' only the Greek Cypriot government in the south would enter the EU.
The resolution was intended to reassure the Greek Cypriot south that the Security Council would fulfill its security obligations under the unity deal.
Contingent on the plan's approval, it would have banned the supply of arms to Cyprus and revamped the UN peacekeeping mission already on the island to help carry out the plan.