Ukrainian MPs also passed a law granting an amnesty to pro-Russian separatists and autonomy to the regions of Donetsk and Luhansk, large areas of which are in rebel hands.The controversial bill, proposed by Mr Poroshenko, was pushed through in a closed session.
While Russia could not prevent the passage of the Association Agreement, its pressure did yield one vital concession.
Ukraine will not begin to implement a free trade area with the EU until the end of next year, although the EU will start to open its own market to Ukrainian goods immediately.
However, politicians in Kiev and Strasbourg were jubilant after the ratification.
It was the refusal of Viktor Yanukovych, then president of Ukraine, to sign this agreement last year that triggered the protests which culminated in his downfall.
Russia then responded by seizing Crimea and inciting rebellion in the eastern regions of Donetsk and Luhansk.
Speaking before the ratification, Petro Poroshenko, the newly elected president of Ukriane, praised the “heavenly 100” demonstrators who were killed during the revolution in February and the soldiers who have died fighting pro-Russian rebels in the east.
He described the passage of the Association Agreement as a vindication of their sacrifice, adding: “They have died not only for their motherland: they gave up their lives for us to take a dignified place among the European family.” The Kremlin bitterly opposed the deal, saying it would damage the Russian economy by undermining Ukrainian demand for its goods.
Martin Schulz, president of the European parliament, described it as “a historic moment” that fulfilled the “dreams of the people who fought for democracy” in Ukraine.
The European Parliament simultaneously ratified the pact by 535 votes to 127.
“Two parliaments doing this at the same time by agreement - that is free democracy, that is free self-determination, that’s the opposite of directed democracy,” added Mr Schulz.
The Kremlin, meanwhile, sees Western backing for Ukraine and other former Soviet states as an attempt to erode Russia’s influence in its traditional sphere.