European Union MPs gave a standing ovation after she made the proposal and then walked over to embrace Canada's Prime Minister Mark Carney, who was in the European Parliament to hear her annual State of the Union address.
New partnerships were needed "in the cold fragility of today's world," von der Leyen told the assembly in Strasbourg, without detailing what associate membership would mean.
The 27-nation bloc faces war at its borders, with Russia's invasion of Ukraine. Both the EU and Canada have also been facing stiff rivalry on trade and other issues from the administration of US President Donald Trump and from an increasingly assertive China.
"I said we must urgently reimagine our partnerships. So, I would like to work with you on opening the door for Canada to be the first associate member of the EU," von der Leyen said.
The EU and Canada "see the world with the same eyes: from AI to climate change, from the Arctic to geopolitics. And we have stood together: on Ukraine, on defence, on raw materials and on supply chains. But above all ... Europe and Canada believe in democracy," von der Leyen told the assembly.
Carney welcomed von der Leyen's proposal for "a far stronger, more ambitious alliance in the future," his office said, adding: "Canada and Europe should secure our strategic autonomy through deep cooperation in the full range of strategic capabilities."
He did not mention associate membership.
It will be up to EU member states, and not von der Leyen alone, whether her proposal, which left some EU watchers befuddled, goes ahead.
The EU has historically resisted flexible alliances that have no legal status. EU members were lukewarm in reacting to Germany's proposal in May of associate membership for Ukraine as a stepping stone to full accession.
One EU diplomat expressed surprise at von der Leyen's proposal, saying "nobody really knows what it means."
The diplomat added there were concerns that the European Commission chief "is overpromising and won't be able to deliver."
Carney's European trip follows the collapse of Canada-US trade talks last month, sparking a series of back-and-forth tariff measures.
He has pledged to double Canada's non-US trade in the next decade as the country pivots away from its southern neighbour amid an increasingly acrimonious trade war.
In her speech, von der Leyen said the EU and Canada will work together across sectors.
"We will work on intelligent manufacturing. We will create a tech alliance. We will integrate defence industrial bases. We will make the Arctic a flagship joint project," she said.
"Partnerships are a strategic choice for Europe. But they also respond to the fracture in the international rules-based system," she added.
Ukraine's Foreign Ministry spokesperson, Heorhii Tykhyi, said his country welcomed deeper ties between the EU and Canada and would closely watch what comes next.
