Speaking in Berlin, the Canadian PM complimented the beleagured German chancellor for her "tremendous" leadership.
He said: "Canada is prroud to call Germany not only a close ally, but a true friend. Building on the values we share and the ties that unite our people.
"CETA is an example of what we can accomplish when our countries work together to deliver real positive results for our citizens."
Justin Trudeau and Angela Merkel in joint press conference
Canada is prroud to call Germany not only a close ally, but a true friend
Justin Trudeau, Canada's PM
The joint press conference came just days after EU politicians ratified the controversial EU-Canada trade deal, which will come into full force in early 2017, when most import duties are to be lifted.
The landmark decision followed a fractious debate between MEPs and mass protests outside the parliament building in Strasbourg on Wednesday.
Supporters say CETA will boost trade between Canada and Europe by 20 per cent and annually £10.2bn (€12bn) to the European Union economy and £7.1bn (€8.4bn) to Canada’s economy.
Speaking about sealing the deal, Mr Trudeau thanked Mrs Merkel for her "steadfast" leadership and support during negotiations and said he hoped he could create a "stronger" relationship with Germany.
He said the ratification of CETA was "a victory that Canadians, Germansand Europeans can share".
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"Progressive trade agreements like this create better paid jobs for our citizens to help generate real growth," he added.
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His comments were echoed by Mrs Merkel who said a worldwide trade deal was “truly beneficial” to “set a standard for future deals to come”.
Mrs Merkel also touched on both countries shared values, by saying: "We have close ties, a friendship, cooperation between our societies. “
The German leader was also quick to comment on the esclating migrant crisis, which is currently engulfing the continent.
She added: "Canada continuously accepts refugees, like we do. We are very grateful to those people that see this as a global mission, a global task. We share the same convictions."
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