Hollande condemned the "odious attack" with "the strongest possible terms" on Monday morning.
"It's the spirit of peace and openness of the people of Quebec that the terrorists wanted to strike," he added.
Two hooded men - one with a strong Quebec accent, according to an eyewitness - opened fire on worshippers in a mosque in Quebec's Sainte-Foy district on Sunday, killing six and wounding eight.
Police said later they had arrested two people, one near the scene of the shooting, the other about 20 kilometres away.
Canadian Prime Minister Justin Trudeau on Monday slammed a "terrorist attack".
"Muslim-Canadians are an important part of our national fabric, and these senseless acts have no place in our communities, city and country," he said.
Quebec in mourning
Quebec Premier Philippe Couillard vowed that the Francophone province would react with "courage and solidarity", while mayor Régis Labeaume sobbed as he declared that the city was "in mourning".
Belgian Prime Minister Charles Michel condemned a "cowardly attack" on Twitter, while EU foreign policy chief Federica Mogherini expressed the European Union's solidarity.
Last summer a pig's head was placed in front of the mosque's doors and similar incidents have taken place at other Muslim places of worship over the last two years.
Two young jihadists carried out attacks in Canada in 2014 and a 24-year-old, who had sworn allegiance to the Islamic State armed group, was killed by police before launching a suicide attack in August last year.