The ceremony in Brussels had been pushed back from Thursday after French-speaking Wallonia, with just 3.6 million people, initially vetoed an agreement affecting more than 500 million Europeans and 35 million Canadians.
Cheers and applause erupted as Trudeau signed the pact alongside EU President Donald Tusk, European Commission head Jean-Claude Juncker and Slovak Prime Minister Robert Fico, whose country holds the rotating EU presidency.
Protesters earlier burst through riot police lines and hurled red paint at the European Union's headquarters, while activists banged drums and chanted slogans against the Comprehensive Economic and Trade Agreement (CETA).
"What patience," replied Juncker, adding: "This is an important day for the EU and for Canada too because we are setting an international standard that will have to be followed by others."
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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.
CETA removes 99 per cent 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.