The free-trade accord is part of the broader EU Association Agreement -- signed at the end of June 2014 -- and stands at the heart of the drastic deterioration of Ukraine's relations with Russia, furious at seeing its Soviet-era satellite turn to the West.
Ukraine, whose market has been traditionally oriented toward Russia, will now have to turn itself toward the European market and abide by its rules.
Brussels also said the deal would help Ukraine improve its business climate and attract foreign investment, a view shared by Yegor Perelygin, an analyst at UniCredit bank.
The road to Ukraine's adoption of the deal has been peppered with obstacles.
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In November 2013, Ukraine's then pro-Kremlin president Viktor Yanukovych rejected the association agreement, triggering pro-European protests that led to his downfall and eventually to the armed conflict in eastern Ukraine, which has left more than 9,000 people dead.
Prime Minister Arseny Yatsenyuk has put the cost of Moscow's measures to his country at some $600 million.
President Petro Poroshenko admitted earlier this month that Russia's retaliatory move would cause "damage" to Ukraine's economy but said he was "ready to pay the price" and press on with efforts to join a European Union free-trade zone.
He blasted the embargo in his New Year address, saying Moscow was trying to "economically strangle" Ukraine.
Kiev has vowed to strike back with its own measures and is expected to announce a list of banned Russian products in the near future.
Ukraine mostly exported agricultural products, vegetables, fruit, dairy and sweets to Russia, with the countries' trade ties shrinking by 70 percent compared to 2011, according to Russia's deputy minister of economic development Alexei Likhachev.