Ukraine’s interim Prime Minister Arseniy Yatsenyuk and the EU signed the deal in Brussels.
Pro-Moscow President Viktor Yanukovych’s abandonment of the deal had led to deadly protests, his removal and Russia taking over Crimea.
On Friday, Russia’s upper house unanimously approved the treaty on Crimea joining the Russian Federation.
The EU Association Agreement is designed to give Ukraine’s interim leadership economic and political support.
EU President Herman Van Rompuy said in a statementthat the accord “recognizes the aspirations of the people of Ukraine to live in a country governed by values, by democracy and the rule of law”.
The move comes hours after the EU broadened its sanctions over Russia’s annexation of Crimea.
It added 12 individuals to an earlier list of 21 who now face asset freezes and travel bans.
The US on Thursday added to its own list and also targeted Rossiya Bank.
Russian Foreign Minister Sergei Lavrov said on Friday the international sanctions were “absolutely unlawful”.
However, Russian President Vladimir Putin said after talks with officials in Moscow that Russia would not take an immediate reciprocal action.
“I think we should refrain from taking steps in response for now,” Interfax quoted Vladimir Putin as saying.
However, Russian PM Dmitry Medvedev said Ukraine should pay back $11 billion in gas discounts as an agreement linked to the lease of the Sevastopol naval base in Crimea was now invalid.
Two credit rating agencies have now downgraded Russia’s outlook to negative from stable.
In Moscow, all 155 senators present in the upper house of parliament voted to ratify the treaty incorporating Crimea into the Russian Federation.
President Vladimir Putin is expected to complete the process by signing the treaty at a ceremony later on Friday.
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