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.