The White House restated its rejection of the referendum in the southern Black Sea region and branded Russia's actions "dangerous and destabilising".
Hinting at additional sanctions, Barack Obama told his Russian counterpart Vladimir Putin the West was ready to "impose additional costs" on Moscow for violating Ukraine's sovereignty.
European diplomats have been drawing up a list of Russian officials who will be hit with travel bans and asset freezes. Foreign ministers are holding an emergency meeting in Brussels today to discuss the sanctions.
President Putin has insisted the vote is legal and promised to "respect" the result.
The referendum saw a landslide in favour of Crimea joining Russia
The final count was 96.77% in favour of joining, said head of the referendum commission Mikhail Malyshev.
Crimea's regional government will make a formal application to join Russia on Monday, its pro-Moscow leader Sergei Aksyonov said on Twitter.
Thousands gathered in the Crimean capital Simferopol ahead of the results, waving Russian and Crimean flags as patriotic songs played and fireworks lit up the sky.
People also turned out to celebrate in Sevastopol, where the Russian navy's Black Sea Fleet is based.
The result was expected as ethnic Russians make up 58% of the population
Lucia Prokorovna, 60, carrying a giant Russian flag said: "We're free of the occupation. Ukraine was attached to Crimea like a sack of potatoes."
The vote, branded illegal by Kiev and Western powers, has triggered the worst East-West crisis since the Cold War and threatens to escalate the crisis in Ukraine.
The intervention of Russian military forces in the region, following the ousting as president of Kremlin ally Viktor Yanukovych last month, led to accusations the poll was conducted "at the barrel of a gun".
Moscow justified the occupation of Crimea, saying it wished to protect the majority ethnic Russian population.
Kiev has accused "Kremlin agents" of stoking violence in Russian-speaking cities such as Donetsk and urged people not to be provoked into retaliating because clashes could be used by Moscow as an excuse for further interventions.
Moscow also raised the stakes after Russian forces, backed by helicopter gunships and armoured vehicles, took control of the Ukrainian village of Strelkovoye and a nearby gas plant.
The Ukraine crisis has led to a Cold War-style stand-off
It was the first Russian military move into Ukraine beyond the Crimean peninsula and while the troops returned the village, they kept control of the gas plant.
Ukrainian Prime Minister Arseniy Yatsenyuk has vowed to bring the Crimean politicians who called the referendum to justice, warning: "The ground will burn under their feet."
In a statement, the White House said: "In this century, we are long past the days when the international community will stand quietly by while one country forcibly seizes the territory of another."
Foreign Secretary William Hague also said the UK would not recognise the outcome of the vote, condemning it as "a mockery of proper democratic practice".
He argued sanctions were needed to "send a strong signal to Russia that this challenge to the sovereignty and territorial integrity of Russia will bring economic and political consequences".
Meanwhile, the EU has decided to impose travel bans and asset freezes against 21 officials from Russia and Ukraine.
At a meeting in Brussels, Foreign Ministers has drawn up a list of Russians to target with sanctions and warned that more could be on the way.
It's after nearly 97 per cent of people in Crimea voted to join Russia.
The Minister for European Affairs Paschal Donohoe says the Irish governent believes the referendum was illegal:
