At a low-key ceremony, in line with requests from the families of the victims for a sober commemoration, Macron was joined by journalists from the magazine, members of his government and the mayor of Paris, Anne Hidalgo.
Two French jihadists who had sworn allegiance to al-Qaeda killed 11 people at Charlie Hebdo's offices in 2015 over the staunchly atheist magazine's satirical coverage of Islam and the prophet Mohammed.
The assault, which saw a policeman executed at pointblank range nearby, profoundly shocked France.
It also marked the beginning of a series of jihadist attacks that have claimed 241 lives in total according to an AFP toll.
Charlie Hebdo, which prides itself on being provocative, returned to the murder of its famed cartoonists and writers in its latest issue.
"The 7th of January 2015 propelled us into a new world of armed police, secure entrances and reinforced doors, of fear and death," wrote contributor Fabrice Nicolino in a column last week.
"And this in the heart of Paris and in conditions which do not honour the French republic. Do we still have a laugh? Yes," he added.
The magazine pays between 1.0-1.5 million euros (1.2-1.8 million dollars) in security costs annually to protect its offices which are at a secret location, its editor Riss wrote.
Sales meanwhile have fallen sharply since a wave of popular support following the bloodshed.
Company revenues fell to 19.4 million euros in 2016, down from more than 60 million in 2015, according to figures first reported by the BFM news channel and confirmed to AFP by the magazine.
Its journalists and editors still regularly receive death threats and the magazine courted fresh controversy in November with a front-page on the Islamic scholar Tariq Ramadan who has been accused of sexually assaulting women.
The Swiss academic, who is widely read and followed in France, was depicted with a huge erection above the line: "I am the sixth pillar of Islam."
The magazine also regularly mocks Christian and Jewish leaders as well as politicians of all stripes.
Two days after the Charlie Hebdo attack, another French extremist took hostages at a Jewish supermarket in eastern Paris, killing five people before elite police raided the premises and shot him dead.
Anti-terror magistrates investigating the incidents are expected to finalise their probe in the next few months but have been unable to determine how the Charlie Hebdo killers -- Cherif and Said Kouchi -- coordinated with the supermarket shooter, Amedy Coulibaly.
They have also failed to track the source of the automatic weapons used by the Kouchi brothers for their killing spree.
This after hundreds gathered in Paris on Saturday as French rights groups commemorated victims of the jihadist attack on French satirical magazine Charlie Hebdo to keep alive the "spirit of Charlie."
Republican and anti-racist groups organised several events on the eve of the third anniversary of the outrage to honour the memory of the 12 people killed in the attack claimed by Al-Qaeda.
The jihadists targeted the staunchly atheist magazine on January 7, 2015 for printing cartoons of the prophet Mohammed, forbidden in Islam.
The murders were the first in a wave of jihadist attacks across France which have left more than 240 people dead.
Among those attending Saturday's events were former prime minister Manuel Valls and Paris mayor Anne Hidalgo, as well as Charlie Hebdo's editor-in-chief Gerard Biard.
The publication lost five cartoonists and three other staff in the attack.
On Sunday, President Emmanuel Macron is due to remember those who died by visiting the Charlie Hebdo offices in the presence of victims' family members.
Four days after the attacks, more than four million people demonstrated across France under the slogan "Je suis Charlie" (I am Charlie) to remember the victims and in support of freedom of expression.
Three years on, the head of international anti-racist organisation LICRA, Mario Stasi, said he felt the "unanimity" of that occasion had dissipated, leading to Saturday's call for a public defence of free speech.
According to an Ifop opinion poll, just 61 percent of French now identify with "Charlie" as they did in the aftermath of the attacks -- ten percent less than in 2015.