It means parts of the deal, such as tariff reduction, will come into force eight years after negotiations began.
But other, more controversial aspects of the deal, such as the investor court system, will require ratification by EU member states which could take years.
There were chaotic scenes outside the parliament building in Strasbourg as protesters blocked access ahead of the vote - only to be dragged off by riot police.
The vote was comfortably, though not overwhelmingly, passed, with 33 members of parliament abstaining.
Ceta`s future was put in temporary doubt last October, when after seven years of talks the small Belgian region of Wallonia vetoed the deal until an addendum was added addressing concerns over the rights of farmers and governments.
The future of the global trade system has also been thrown into question by the election of US President Donald Trump - who has withdrawn from the Trans-Pacific Partnership (TPP) and wants to renegotiate the North American Free Trade Agreement (Nafta).
The result was celebrated by backers of the deal - including Jyrki Katainen, European Commission vice-president for jobs, growth, investment and competitiveness.
But opponents - such as Guido Tallman, a campaigner for the UK group Global Justice UK - pointed out that its full implementation would require ratification by dozens of regional and national parliaments.
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