The United States has welcomed the move, saying it fulfills the will of the Ukranian people and shows the Ukrainian government is committed to a peaceful solution to the country's crisis.
Ukrainian Prime Minister Arseny Yatseniuk says the pact rights an historic wrong.
"A vote for today's ratification is a choice of the civilisation for Ukraine. We are correcting a mistake that was made 350 years ago. Ukraine is Europe," he said.
"That's what the Ukrainian people said and did. The signature of the whole of Ukraine is under this agreement."
The EU pact had been rejected by former pro-Russian president Viktor Yanukovych in November last year, in favour of closer ties with Ukraine's ex-Soviet master, Russia. His retreat triggered months of street protests and sparked a chain of events that provoked the worst crisis between Russia and the West since the Cold War.
More than 3,000 have been killed in the conflict since November, which resulted in the United States and its Western allies imposing sanctions against Moscow.
Leaders in Kiev also voted to allow independence to separatists in the country's east. The measure was part of a peace plan agreed to over a week ago to end the bloodshed between the government and those thought to be pro-Russian forces, since their seizure of eastern regions bordering Russia in April.
Ukraine's President Petro Poroshenko says offering a limited but "special status" to the separatists was about building peace.
"I am convinced that today we have achieved the situation when the peace process has not been derailed, that today I have no doubt that we have come closer to a situation where people in the east of Ukraine will stop dying and that finally people living in Donetsk and Luhansk should have an opportunity to elect new authorities," he said.
But Russia has signalled it has no intention of backing down, announcing an increase of troops in annexed Crimea.
Almost 30 Ukrainian civilians and soldiers have reportedly been killed since a tenuous truce in the region came into force on the 5th of September.
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