Nearly 5,000 mourners packed into a hockey arena in Montreal's Olympic park for the funeral, while many more across Canada watched it on television.
For many in this mostly secular nation, the ceremony was their first glimpse of traditional Muslim funeral rites.
There were also prayers for the other three victims, who will be commemorated the next day in Quebec City.
Khaled Belkacemi, 60, and Abedlkrim Hassane, 41, both Algerian dual nationals, and Tunisian-born Aboubaker Thabti, 44, were shot dead, along with three other worshippers at a Quebec City mosque on Sunday.
"The pain is hard to express, it runs deep," mourner Mohamed Lemdani told AFP.
"We are all family men who came to Canada to work and integrate into a multicultural society," he said.
White flower wreaths were placed by the coffins, covered by the flags of the victims' birth countries, where their bodies later would be transported for burial.
There has been an outpouring of support for Canada's minority Muslim community in the wake of the attack, but also pockets of increased hate mongering.
At the funeral Catholics, Jews, Muslims and agnostics sat side by side, hugging each other and wiping away tears as verses of the Koran were read aloud.
"The whole nation has been shaken by this brutal and hateful attack, but in these dark moments our country has united and showed solidarity," said Trudeau.
"(Say) no to violence, no to intimidation, racism and xenophobia," said Quebec Premier Philippe Couillard.
To Canada's 1.1 million-strong Muslim minority, he said: "Know that you are at home here."
Community fears
Despite reassurances, the attack that left 17 children orphaned has provoked fear in the Muslim community, noted Said Fawaz, president of the Quebec Council of Imams.
He called on Muslims not to cower.
"Muslims must not recoil and isolate themselves as our neighbor to the south would like us to do," he said, alluding to US President Donald Trump's order banning entry to refugees and migrants from seven Muslim-majority nations.
The attack came as a shock to Canada -- a fierce defender of multiculturalism -- revealing cracks in its social fabric where racist movements have sprouted.
A little more than a year ago, Trudeau himself greeted the first of 40,000 Syrian refugees resettled in Canada, handing out parkas with a smile.
On Wednesday, a member of his Liberal Party apologized in parliament to Canadian Muslims for having not done enough to discourage bigotry.
"I ask them for forgiveness for having observed their ostracization and stigmatization in recent years, to have watched take root in the hearts of my fellow men fear, mistrust and hatred... (and) to have not done enough to answer it," said MP Joel Lightbound.
"If words have consequences, silences also have consequences," he said.
The victims were a scholar, a butcher, a daycare operator, a food industry worker, a public servant and a computer programmers -- all connected by faith.
All of them were said to have emigrated to Canada to raise families in peace and prosperity, some after fleeing violence in their homeland.
They had been attending evening prayers at their mosque in Quebec City when a 27-year-old gunman stormed in and unleashed a barrage of bullets from a pistol and semi-automatic rifle.
The suspect later surrendered to police and was charged with six murders and five attempted murders.
Friday morning, a second funeral will be held in Quebec City for the other three victims, Guinean-Canadians Mamadou Tanou Barry, 42, and Ibrahima Barry, 39, and Azzeddine Soufiane, of Moroccan origin and 57 years old, who had lived in Quebec for 30 years.
Burial arrangements for the trio have not yet been confirmed.
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