The ceremony had been pushed back from Thursday after French-speaking Wallonia, with just 3.6 million people, initially vetoed a deal affecting more than 500 million Europeans and 35 million Canadians.
Protesters today threw red paint at the European Union's headquarters, banged drums and chanted slogans as Trudeau arrived to meet EU President Donald Tusk and European Commission chief Jean-Claude Juncker.
"Well done, well done," Trudeau said as he hugged and kissed Tusk and Juncker on his arrival amid tight security. "Things were difficult but we managed to succeed in the end."
The start of today's summit was further delayed when Trudeau's plane was briefly forced to turn back due to mechanical problems, capping two weeks of chaos over what was meant to be a symbolic sign-off.
Formally known as the Comprehensive Economic and Trade Agreement (CETA), the deal removes 99 percent of customs duties between the two sides, linking the single EU market with the world's 10th largest economy.
After years of negotiations the deal almost collapsed, with Trudeau only agreeing late Friday to fly to Brussels after Wallonia finally agreed to join the rest of Belgium and the other 27 EU member states in approving the deal.
The pact required all EU member states to endorse it and in some cases such as Belgium's for regional governments to agree too, giving tiny Wallonia an effective veto.
The concerns in the declining industrialised region in Belgium's south reflected wider concerns in Europe about globalisation, as well as fears among activists that such deals erode consumer, social and environmental protections.
Belgian Foreign Minister Didier Reynders said "nothing is simple in Belgium but few things are impossible" as he officially signed up to the deal on Saturday.
Belgian Prime Minister Charles Michel insisted that the marathon talks with Wallonia "did not change a comma" in the deal. But Walloon government head Paul Magnette said he received assurances from the federal government of strengthened social and environmental protections.
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