Russia had worked aggressively to derail the deal by imposing painful trade sanctions and threatening Ukraine with giant gas bills.
And Ukraine knows what Russian pressure feels like.
Moscow had previously cut off gas supplies during bitter pricing disputes to leave Ukrainians freezing in the depth of winter. Now, it is offering Ukraine much-needed discounts for its natural gas in exchange for joining a Moscow-led Customs Union.
Although the European Union extended its geopolitical reach eastward by initialing agreements with Georgia and Moldova during the two-day summit, Ukraine was a blow.
"We may not give in to external pressure, not the least from Russia," said EU President Herman Van Rompuy in unusually blunt terms after Yanukovych refused to put ink to paper.
Yanukovych's move sparked mass protests in the Ukranian capital on Friday.
Such large demonstrations haven't been seen since 2004 during what has become known as the Orange Revolution, which led to the overturn of Yanukovych's fraud-marred election victory and brought his pro-Western opponent to power. Yanukovych is wary of a repeat.
"Millions of Ukrainians don't want to return to the Soviet past," said Olga Shukshina, a 46-year-old doctor from the Western city of Lviv, close to the border with Poland.
World boxing champion and opposition leader, Vitaly Klitshcko, called for more protests.
"I am sure we will lead Ukraine into Europe even without Yanukovych," Klitshcko said in Vilnius. "This is our task, the task of the opposition forces, and the task of every Ukrainian."
In Moscow, Sergei Naryshkin, the speaker of the Kremlin-controlled lower house of Russian parliament, harshly criticized the EU for sending special envoys to Ukraine as its parliament pondered closer ties with the West.
"We have witnessed an unprecedented pressure on Ukraine from Western nations," Naryshkin said.
EU Commission President Jose Manuel Barroso complained about Russia's trade threats and said "the times for limited sovereignty are over in Europe," alleging Russia still seemed to consider Ukraine as a subservient neighbor.
Such talk was rife in the decades after World War II when the West and the Soviet Union faced off and carved up central Europe in their own spheres of influence, robbing many east European nations of their full independence.
Ukraine looms especially large in Moscow's eyes, much more so than Georgia or Moldova. President Vladimir Putin has spoken of Ukraine as the cradle of the Russian state, and of the two countries as "one nation."
Yanukovych is now seeking a trilateral deal which would also include Russia, a notion the EU immediately dismissed. "When we make a bilateral deal, we don't need a trilateral agreement," said Barroso.
German Chancellor Angela Merkel lauded Georgia and Moldova for withstanding similar pressure and still moving westward.
After seeing Ukraine bow out of the deal, Georgian President Giorgi Margvelashvili told The Associated Press in an interview that he is preparing to resist Russian pressure as the deal moves from Friday's technical approval to full signature in the months ahead.
"We acknowledge that we have to be very mobilized and very organized for possible complications on our path," Margvelashvili said.
- AP